Far-red Sun-induced Chlorophyll Fluorescence Research Articles

Ground far-red sun-induced chlorophyll fluorescence and vegetation indices in the US Midwestern agroecosystems

Sun-induced chlorophyll fluorescence (SIF) provides an opportunity to study terrestrial ecosystem photosynthesis dynamics. However, the current coarse spatiotemporal satellite SIF products are challenging for mechanistic interpretations of SIF signals. Long-term ground SIF and vegetation indices (VIs) are important for satellite SIF validation and mechanistic understanding of the relationship between SIF and photosynthesis when combined with leaf- and canopy-level auxiliary measurements. In this study, we present and analyze a total of 15 site-years of ground far-red SIF (SIF at 760 nm, SIF760) and VIs datasets from soybean, corn, and miscanthus grown in the U.S. Corn Belt from 2016 to 2021. We introduce a comprehensive data processing protocol, including different retrieval methods, calibration coefficient adjustment, and nadir SIF footprint upscaling to match the eddy covariance footprint. This long-term ground far-red SIF and VIs dataset provides important and first-hand data for far-red SIF interpretation and understanding the mechanistic relationship between far-red SIF and canopy photosynthesis across various crop species and environmental conditions.

Prediction of Open Woodland Transpiration Incorporating Sun-Induced Chlorophyll Fluorescence and Vegetation Structure

Transpiration (T) represents plant water use, while sun-induced chlorophyll fluorescence (SIF) emitted during photosynthesis, relates well to gross primary production. SIF can be influenced by vegetation structure, while uncertainties remain on how this might impact the relationship between SIF and T, especially for open and sparse woodlands. In this study, a method was developed to map T in riverine floodplain open woodland environments using satellite data coupled with a radiative transfer model (RTM). Specifically, we used FluorFLiES, a three-dimensional SIF RTM, to simulate the full spectrum of SIF for three open woodland sites with varying fractional vegetation cover. Five specific SIF bands were selected to quantify their correlation with field measured T derived from sap flow sensors. The coefficient of determination of the simulated far-red SIF and field measured T at a monthly scale was 0.93. However, when comparing red SIF from leaf scale to canopy scale to predict T, performance declined by 24%. In addition, varying soil reflectance and understory leaf area index had little effect on the correlation between SIF and T. The method developed can be applied regionally to predict tree water use using remotely sensed SIF datasets in areas of low data availability or accessibility.

Development of a filter-based near-surface remote sensing system to retrieve far-red sun-induced chlorophyll fluorescence

Observations of sun-induced chlorophyll fluorescence (SIF) by remote sensing have improved our understanding of the structural and physiological dynamics of vegetation. Substantial efforts have been made to measure SIF with ground-based sensing systems, but field observation data for various plant functional types are still sparse. This is partly due to the limited availability of commercial SIF measurement systems, the relatively high cost of hyperspectral spectroradiometers, and the difficulties of sensor calibration and maintenance in the field. We developed a filter-based smart near-surface remote sensing system for SIF (4S-SIF) to overcome the technical challenges of monitoring SIF in the field, which also decreased the sensor cost, thus enabling more comprehensive spatial sampling. To retrieve SIF, we combined ultra-narrow bandpass filters (full width half maximum <1.3 nm) and photodiode detectors to observe electromagnetic radiation at specific wavelengths (757, 761, and 770 nm). We confirmed that the spectral and radiometric performance of the bandpass filters was satisfactory to retrieve SIF by comparing them to a high-spectral-resolution spectroradiometer that served as a reference. In particular, we confirmed that the digital numbers (DNs) from 4S-SIF exhibited linear relationships with the DN from the reference spectroradiometer in each band (R2 > 0.99). In addition, we developed equations to correct for temperature-induced changes in filter transmittance, such that SIF can be reliably extracted in outdoor environments without the need to actively stabilize the temperature. Furthermore, we confirmed that the SIF signal from 4S-SIF had a strong linear relationship with the reference spectroradiometer-based SIF. Importantly, this relationship held even when the physiological mechanisms of the plant were altered by a herbicide treatment that induced substantial changes in the SIF signal (R2 = 0.85, relative RMSE = 0.22), which indicated that 4S-SIF could be used to retrieve SIF. We believe that 4S-SIF will be a useful tool for collecting in-situ SIF data across multiple spatial and temporal scales.

A precise method unaffected by atmospheric reabsorption for ground-based retrieval of red and far-red sun-induced chlorophyll fluorescence

Remote sensing employs solar-induced chlorophyll fluorescence (SIF) as a proxy for photosynthesis from field to airborne and satellite sensors. The investigation of SIF offers a unique way of studying vegetation functioning from the local to the global scale. However, the passive, optical retrieval of the SIF signal is still challenging. Common retrieval approaches extract the SIF infilling directly from atmospheric oxygen bands in down-welling and up-welling radiance. They often involve a complex signal correction to compensate for atmospheric reabsorption and require long computing time. In contrast, the exploitation of solar Fraunhofer lines is devoid of atmospheric disturbances. We propose a new retrieval method for red and far-red SIF directly from up-welling radiance spectra in the spectral range between 650 nm and 810 nm by applying Partial Least Squares (PLS) regression machine learning. Solar Fraunhofer lines are exploited for SIF retrieval with the PLS approach by excluding telluric absorption features. The PLS models are trained and tested on synthetic reflectance and SIF data modeled with SCOPE. We identified a logarithmic relationship of the retrieval error with respect to signal-to-noise ratio of the instrument. The approach has been tested with real-world data measured by the Fluorescence Box (FloX), and evaluated against two well-established retrieval methods: the spectral fitting method (SFM) and the singular value decomposition (SVD). PLS models exploiting solar Fraunhofer lines retrieved meaningful SIF values with high precision and demonstrated robustness against atmospheric reabsorption, including from a 100m tall tower. In addition, PLS retrieval requires no complex correction for atmospheric reabsorption and computes 37 times faster than SFM. Hence, PLS retrieval allows fast and robust exploitation of SIF from solar Fraunhofer lines with high precision under conditions in which other retrieval approaches require complex atmospheric correction.

Comparison of a UAV- and an airborne-based system to acquire far-red sun-induced chlorophyll fluorescence measurements over structurally different crops

• Pronounced diurnal patterns found for both UAV- and Airborne-based far-red SIF. • Consistent spatial patterns of UAV- and Airborne-based far-red SIF over different crops. • FluorSpec far-red SIF is linearly related to HyPlant far-red SIF. • Far-red sun-induced chlorophyll fluorescence can be reliably measured from a UAV. Sun-induced chlorophyll fluorescence (SIF) is a promising proxy of the dynamic photosynthetic process. Unmanned Aerial Vehicles (UAVs) are flexible and cost-effective for acquiring SIF data at high temporal and spatial resolution. The UAV-based point spectrometer FluorSpec was designed to measure SIF within agricultural fields. To correctly understand SIF values and further photosynthetic research, the ability of the UAV-based FluorSpec to provide reliable SIF information within agricultural fields needs evaluation. In this paper, the UAV-based FluorSpec was compared with the high-performance airborne imaging spectrometer HyPlant using diurnal far-red SIF measurements over different crop types (i.e. two varieties of winter wheat, two varieties of spring barley, bean, and maize), which were acquired by almost simultaneous airborne and UAV flights during a clear sky day in 2019. After improving the footprint geolocation of FluorSpec measurements using concurrent red-green-blue (RGB) images, we compared the FluorSpec and HyPlant SIF measurements, their diurnal developments, and spatial distributions for different crop types. The results from both systems show consistent, clear diurnal patterns that are positively correlated with photosynthetically active radiation (PAR) over most crop types. Similar SIF spatial patterns were shown within crop fields as well. UAV-based FluorSpec SIF showed a good linear correlation with HyPlant SIF with an R 2 up to 0.76. The good agreement confirms that the UAV-based FluorSpec system is able to measure meaningful SIF values at the field scale and thus stimulates SIF applications in agriculture. The systematic errors up to 0.3 mW m −2 sr −1 nm −1 from the linear regression between the two systems indicate that the UAV-based FluorSpec system should be improved by considering the main sources of uncertainty discussed in this paper. Future studies with dedicated experiments are recommended to assess the systematic uncertainties of UAV-based FluorSpec derived SIF information.

Response times of remote sensing measured sun-induced chlorophyll fluorescence, surface temperature and vegetation indices to evolving soil water limitation in a crop canopy

Vegetation responds at varying temporal scales to changing soil water availability. These process dynamics complicate assessments of plant-water relations but also offer various access points to advance understanding of vegetation responses to environmental change. Remote sensing (RS) provides large capacity to quantify sensitive and robust information of vegetation responses and underlying abiotic change driver across observational scales. Retrieved RS based vegetation parameters are often sensitive to various environmental and plant specific factors in addition to the targeted plant response. Further, individual plant responses to water limitation act at different temporal and spatial scales, while RS sampling schemes are often not optimized to assess these dynamics. The combination of these aspects complicates the interpretation of RS parameter when assessing plant-water relations. We consequently aim to advance insight on the sensitivity of physiological, biochemical and structural RS parameter for plant adaptation in response to emerging soil water limitation. We made a field experiment in maize in Tuscany (Central Italy), while irrigation was stopped in some areas of the drip-irrigated field. Within a period of two weeks, we measured the hydraulic and physiological state of maize plants in situ and complemented these detailed measurements with extensive airborne observations (e.g. sun-induced chlorophyll fluorescence (SIF), vegetation indices sensitive for photosynthesis, pigment and water content, land surface temperature). We observe a double response of far-red SIF with a short-term increase after manifestation of soil water limitation and a decrease afterwards. We identify different response times of RS parameter representing different plant adaptation mechanisms ranging from short term responses (e.g. stomatal conductance, photosynthesis) to medium term changes (e.g. pigment decomposition, changing leaf water content). Our study demonstrates complementarity of common and new RS parameter to mechanistically assess the complex cascade of functional, biochemical and structural plant responses to evolving soil water limitation.

NIRVP: A robust structural proxy for sun-induced chlorophyll fluorescence and photosynthesis across scales

Sun-induced chlorophyll fluorescence (SIF) is a promising new tool for remotely estimating photosynthesis. However, the degree to which incoming solar radiation and the structure of the canopy rather than leaf physiology contribute to SIF variations is still not well characterized. Therefore, we investigated relationships between SIF and variables that at least partly capture the canopy structure component of SIF. For this, we relied on high-quality SIF observations from ground-based instruments, high-resolution airborne SIF imagery and the most recent satellite SIF products to cover large ranges in spatial and temporal resolution and diverse ecosystems. We found that the canopy structure-related near-infrared reflectance of vegetation multiplied by incoming sunlight (NIRVP) is a robust proxy for far-red SIF across a wide range of spatial and temporal scales. Our findings indicate that contributions from leaf physiology to SIF variability are small compared to the structure and radiation components. Also, NIRVP captured spatio-temporal patterns of canopy photosynthesis better than SIF, which seems to be mostly due to the greater retrieval noise of SIF. Compared to other relevant structural SIF proxies, NIRVP showed more robust relationships to SIF, especially at the global scale. Our results highlight the promise of using widely available NIRVP data for vegetation monitoring and also indicate the potential of using SIF and NIRVP in combination to extract physiological information from SIF.

Uncertainty analysis of SVD-based spaceborne far–red sun-induced chlorophyll fluorescence retrieval using TanSat satellite data

The singular value decomposition (SVD) method, a sun-induced chlorophyll fluorescence (SIF) retrieval approach, has been used widely in far-red SIF spaceborne retrievals on a global scale. However, due to its semi-empirical nature, setting different parameter values may affect its retrieval accuracy, and ultimately have a large impact on its application. Hence, in this study, we evaluated the impact of parameter selection on the far-red SIF retrieval of this approach using TanSat satellite data. We first retrieved the far-red SIF within a narrow spectral window of 757.4–759.2 nm using the first four singular vectors (SVs) that were derived from the snow and soil spectra in a globally distributed training set. The retrievals are highly consistent with TanSat mission SIF (R2 = 0.72), indicating the reliability of our retrieval results. Then, the uncertainty was executed based on the above SIF retrievals and evaluated from five metrics: the number of SVs, length of the fitting window, type of training set elements, proportion of training set elements, and spatial distribution of the training set. Results showed that an unwise selection of the number of SVs would result in large retrieval errors (R2 = 0.03). Meanwhile, a fitting window that is too short or does not include a strong Fraunhofer line would cause severe errors and a large number of negative values (R2 = 0.06). Further, failure to include training samples below the equatorial zone in the Southern Hemisphere, and high latitude samples in the Northern Hemisphere, leads to poorer outcomes (R2 = 0.57). In contrast, the other global sampling metrics had little effect on the retrieval results (generally, R2 > 0.97). Accordingly, the relevant suggestions for using this method in the future are listed in this study for reference, with the potential to improve the accuracy of SIF retrievals from ultra-high spectral resolution instruments in the far-red spectrum.

Enhanced drought detection and monitoring using sun-induced chlorophyll fluorescence over Hulun Buir Grassland, China

Drought is one of the most damaging events in the grassland ecosystem. The detection and monitoring of drought are very important to maintain the balance of the grassland ecosystem. The potential of Sun-induced Chlorophyll Fluorescence (SIF) for drought detection and monitoring were explored in this study. Based on significant negative anomalies of self-calibrating Palmer drought severity index (scPDSI), precipitation (PPT), soil moisture (SM)，surface water storage (SWS), and a significant positive anomaly of land surface temperature (LST), a severe drought event was accurately detected from June to August in 2016 over Hulun Buir Grassland. The far-red SIF was decomposed into its mechanical parts such as SIF, absorbed photosynthetically active radiation (APAR), normalized by APAR (SIFyield), physiological SIF emission yield (SIFpey), and total emitted SIF (SIFte), which were more sensitive to drought than the vegetation indices (VIs), including normalized difference vegetation index (NDVI), enhanced vegetation index (EVI), modified soil adjusted vegetation index (MSAVI2), and near-infrared reflectance of vegetation (NIRV). SIF and NIRV represented the SIF indicators and the VIs, respectively, which were most affected by drought, with a decrease of −2.67% and 4.19% in June, 50.93% and 31.76% in July, and 55.58% and 39.44% in August. The correlations between anomalies of SIF indicators, VIs, and anomalies of LST, wind speed (WS) were a strong negative correlation, indicating that their reduction was caused by the anomalies of LST and WS. Moreover, the SIF indicators had a shorter lag time in response to meteorological drought than VIs. Besides, the correlations between SIF-based drought indices such as drought fluorescence monitoring index (DFMI), SIF health index (SHI), and SM were − 0.709 and − 0.783 (P < 0.01), respectively, higher than the conventional drought indices. Moreover, DFMI and SHI could reflect the changes of SM in advance, while the conventional drought indices mostly lagged behind the changes of SM. This study shows that SIF can enhance drought detection, and the SIF-based drought index can be well suitable for drought monitoring.

Unraveling the physical and physiological basis for the solar- induced chlorophyll fluorescence and photosynthesis relationship using continuous leaf and canopy measurements of a corn crop

Abstract. Estimates of the gross terrestrial carbon uptake exhibit large uncertainties. Sun-induced chlorophyll fluorescence (SIF) has an apparent near-linear relationship with gross primary production (GPP). This relationship will potentially facilitate the monitoring of photosynthesis from space. However, the exact mechanistic connection between SIF and GPP is still not clear. To explore the physical and physiological basis for their relationship, we used a unique data set comprising continuous field measurements of leaf and canopy fluorescence and photosynthesis of corn over a growing season. We found that, at canopy scale, the positive relationship between SIF and GPP was dominated by absorbed photosynthetically active radiation (APAR), which was equally affected by variations in incoming radiation and changes in canopy structure. After statistically controlling these underlying physical effects, the remaining correlation between far-red SIF and GPP due solely to the functional link between fluorescence and photosynthesis at the photochemical level was much weaker (ρ=0.30). Active leaf level fluorescence measurements revealed a moderate positive correlation between the efficiencies of fluorescence emission and photochemistry for sunlit leaves in well-illuminated conditions but a weak negative correlation in the low-light condition, which was negligible for shaded leaves. Differentiating sunlit and shaded leaves in the light use efficiency (LUE) models for SIF and GPP facilitates a better understanding of the SIF–GPP relationship at different environmental and canopy conditions. Leaf level fluorescence measurements also demonstrated that the sustained thermal dissipation efficiency dominated the seasonal energy partitioning, while the reversible heat dissipation dominated the diurnal leaf energy partitioning. These diurnal and seasonal variations in heat dissipation underlie, and are thus responsible for, the observed remote-sensing-based link between far-red SIF and GPP.

Adjustments to SIF Aid the Interpretation of Drought Responses at the Caatinga of Northeast Brazil

Sun-Induced chlorophyll Fluorescence (SIF) relates directly to photosynthesis yield and stress but there are still uncertainties in its interpretation. Most of these uncertainties concern the influences of the emitting vegetation’s structure (e.g., leaf angles, leaf clumping) and biochemistry (e.g., chlorophyll content, other pigments) on the radiative transfer of fluorescent photons. The Caatinga is a large region in northeast Brazil of semiarid climate and heterogeneous vegetation, where such biochemical and structural characteristics can vary greatly even within a single hectare. With this study we aimed to characterize eleven years of SIF seasonal variation from Caatinga vegetation (2007 to 2017) and to study its responses to a major drought in 2012. Orbital SIF data from the instrument GOME-2 was used along with MODIS MAIAC EVI and NDVI. Environmental data included precipitation rate (TRMM), surface temperature (MODIS) and soil moisture (ESA CCI). To support the interpretation of SIF responses we used red and far-red SIF adjusted by the Sun’s zenith angle (SIF-SZA) and by daily Photosynthetically Active Radiation (dSIF). Furthermore, we also adjusted SIF through two contrasting formulations using NDVI data as proxy for structure and biochemistry, based on previous leaf-level and landscape level studies: SIF-Yield and SIF-Prod. Data was tested with time-series decomposition, rank correlation, spatial correlation and Linear Mixed Models (LMM). Results show that GOME-2 SIF and adjusted SIF formulations responded consistently to the observed environmental variation and showed a marked decrease in SIF emissions in response to a 2012 drought that was generally larger than the corresponding NDVI and EVI decreases. Drought sensitivity of SIF, as inferred from LMM slopes, was correlated to land cover at different regions of the Caatinga. This is the first study to show correlation between landscape-level SIF and an emergent property of ecosystems (i.e., resilience), showcasing the value of remotely sensed fluorescence for ecological studies.

Sun–induced fluorescence heterogeneity as a measure of functional diversity

Plant functional diversity, defined as the range of plant chemical, physiological and structural properties within plants, is a key component of biodiversity which controls the ecosystem functioning and stability. Monitoring its variations across space and over time is critical in ecological studies. So far, several reflectance-based metrics have been tested to achieve this objective, yielding different degrees of success. Our work aimed at exploring the potential of a novel metric based on far-red sun-induced chlorophyll fluorescence (F760) to map the functional diversity of terrestrial ecosystems. This was achieved exploiting high-resolution images collected over a mixed forest ecosystem with the HyPlant sensor, deployed as an airborne demonstrator of the forthcoming ESA-FLEX satellite. A reference functional diversity map was obtained applying the Rao's Q entropy metric on principal components calculated on key plant functional trait maps retrieved from the hyperspectral reflectance cube. Based on the spectral variation hypothesis, which states that the biodiversity signal is encoded in the spectral heterogeneity, two moving window-based approaches were tested to estimate the functional diversity from continuous spectral data: i) the Rao's Q entropy metric calculated on the normalized difference vegetation index (NDVI) and ii) the coefficient of variation (CV) calculated on hyperspectral reflectance. Finally, a third moving window approach was used to estimate the functional diversity based on F760 heterogeneity quantified through the calculation of the Rao's Q entropy metric.Results showed a strong underestimation of the functional diversity using the Rao's Q index based on NDVI and the CV of reflectance. In both cases, a weak correlation was found against the reference functional diversity map (r2 = 0.05, p < .001 and r2 = 0.04, p < .001, respectively). Conversely, the Rao's Q index calculated on F760 revealed similar patterns as the ones observed in the reference map and a better correlation (r2 = 0.5, p < .001). This corroborates the potential of far-red F for assessing the functional diversity of terrestrial ecosystems, opening unprecedented perspectives for biodiversity monitoring across different spatial and temporal scales.

Canopy structure explains the relationship between photosynthesis and sun-induced chlorophyll fluorescence in crops

Remote sensing of far-red sun-induced chlorophyll fluorescence (SIF) has emerged as an important tool for studying gross primary productivity (GPP) at the global scale. However, the relationship between SIF and GPP at the canopy scale lacks a clear mechanistic explanation. This is largely due to the poorly characterized role of the relative contributions from canopy structure and leaf physiology to the variability of the top-of-canopy, observed SIF signal. In particular, the effect of the canopy structure beyond light absorption is that only a fraction (fesc) of the SIF emitted from all leaves in the canopy can escape from the canopy due to the strong scattering of near-infrared radiation. We combined rice, wheat and corn canopy-level in-situ datasets to study how the physiological and structural components of SIF individually relate to measures of photosynthesis. At seasonal time scales, we found a considerably strong positive correlation (R2 = 0.4–0.6) of fesc to the seasonal dynamics of the photosynthetic light use efficiency (LUEP), while the estimated physiological SIF yield was almost entirely uncorrelated to LUEP both at seasonal and diurnal time scales, with the partial exception of wheat. Consistent with these findings, the canopy structure and radiation component of SIF, defined as the product of APAR and fesc, explained the relationship of observed SIF to GPP and even outperformed GPP estimation based on observed SIF at two of the three sites investigated. These results held for both half-hourly and daily mean values. In contrast, the total emitted SIF, obtained by normalizing observed SIF for fesc, improved only the relationship to APAR but considerably decreased the correlation to GPP for all three crops. Our findings demonstrate the dominant role of canopy structure in the SIF-GPP relationship and establish a strong, mechanistic link between the near-infrared reflectance of vegetation (NIRV) and the relevant canopy structure information contained in the SIF signal. These insights are expected to be useful in improving remote sensing based GPP estimates.

Fluorescence Correction Vegetation Index (FCVI): A physically based reflectance index to separate physiological and non-physiological information in far-red sun-induced chlorophyll fluorescence

Sun-induced chlorophyll fluorescence (SIF) has been used to track vegetation photosynthetic activity for improving estimation of gross primary productivity (GPP) and detecting plant stress. There are both physical and physiological controls of SIF measured at the surface and retrieved from remote sensing including satellite observations. In order to accurately use SIF for monitoring of plant physiology, the effects of physically-based radiation processes related to leaf and canopy structure, notably photosynthetically active radiation (PAR) absorption and SIF scattering and re-absorption, must be characterized. In this study, we investigate both PAR absorption and SIF scattering processes and find that although it is difficult to quantify their effects individually by using just reflectance, the combined effects of the two processes can be well approximated by a reflectance index. This index, referred to as FCVI (Fluorescence Correction Vegetation Index), is defined as the difference between near-infrared (NIR) and broad-band visible (VIS, 400–700 nm) reflectance acquired under identical sun-canopy-observer geometry of the SIF measurements. The development of the index was based on the physical connection between reflectance and far-red SIF, which was revealed by using the spectral invariant theory. The utility of FCVI to correct far-red SIF for PAR absorption and scattering effects, thus improving the link to photosynthesis, was tested with data from: (i) a field experiment for a growing season; and (ii) a numerical experiment which included a number of scenarios generated by a radiative transfer model. For both the observations and simulations, the FCVI provided a promising estimate of the impact of the physically-based radiation processes on far-red SIF of moderately dense canopies (i.e., FCVI ≥ 0.18). Normalizing the TOC far-red SIF by both the incident PAR (iPAR) and the FCVI provided a good estimate of the far-red fluorescence emission efficiency of the canopies examined. This approach enhances our ability to generalize retrievals for vegetation processes as they change through natural growth phases and seasons. Taken together, far-red SIF and FCVI may enable the assessment of the light partitioning of vegetation canopies, an essential step to facilitate the use of far-red SIF for tracking physiological processes.

Making full use of hyperspectral data for gross primary productivity estimation with multivariate regression: Mechanistic insights from observations and process-based simulations

Statistical gross primary productivity (GPP) estimation from remote sensing observations has mostly been attempted on the basis of multispectral observations. To make full use of the information contained in vegetation spectra, however, hyperspectral observations should be used in combination with appropriate multivariate methods. Nevertheless, only very few previous studies attempted to estimate GPP directly from hyperspectral observations and did so on the basis of reflectance, with only a limited number of temporally discontinuous observations. In this study, we used long-term, continuous, half-hourly hyperspectral observations covering the visible and near-infrared spectral range to estimate GPP directly from upwelling irradiance using partial least square (PLS) regression in a rice paddy. To gain a better understanding of processes underlying the PLS estimation, we used extensive complementary field observations to run process-based simulations using the SCOPE model. We then applied PLS regression to the simulated hyperspectral data in the same way as for the observations and disentangled contributions related to relevant physiological processes, namely sun-induced chlorophyll fluorescence (SIF) and xanthophyll cycle-related spectral changes (XC). We found that upwelling hyperspectral irradiance in the visible and near-infrared spectral range predicted GPP better than reflectance. Furthermore, PLS-based GPP estimates outperformed both far-red SIF and widely used vegetation index-based methods. However, the most relevant information for the observation-based PLS-models was not clearly related to XC or SIF as the near-infrared spectral range showed comparable performance. Also, the simple average of upwelling irradiance over the 850–900 nm range outperformed the other non-multivariate approaches, including far-red SIF. These results held for the evaluation in terms of the seasonal variation of GPP, while there was apparently a small contribution of SIF and XC for the diurnal variation. The simulation-based analysis showed that SIF and XC contributed useful information to both GPP and photosynthetic light use efficiency (LUE) estimates at both seasonal and diurnal time scales. The strongest unique contribution from either SIF or XC, however, was to the diurnal variation of GPP and XC showed considerably better performance than SIF. We did not find improvements when combining the spectral regions of XC (500–570 nm) and SIF (650–800 nm) to estimate GPP. While SIF showed improvements when combined with the remaining spectral information excluding XC, this was not the case for XC. Our approach combines the strengths of process-based modeling with multivariate statistical analysis to improve our understanding of the usable information content in vegetation spectra and is highly relevant for further developing suitable methods for GPP estimation at large scales.

Using reflectance to explain vegetation biochemical and structural effects on sun-induced chlorophyll fluorescence

The growing availability of global measurements of sun-induced chlorophyll fluorescence (SIF) can help in improving crop monitoring, especially the monitoring of photosynthetic activity. However, variations in top-of-canopy (TOC) SIF cannot be directly interpreted as physiological changes because of the confounding effects of vegetation biochemistry (i.e. pigments, dry matter and water) and structure. In this study, we propose an approach of using radiative transfer models (RTMs) and TOC reflectance to estimate the biochemical and structural effects on TOC SIF, as a necessary step in retrieving physiological information from TOC SIF. The approach was assessed by using airborne (HyPlant) reflectance and SIF data acquired over an agricultural experimental farm in Germany on two days, before and during a heat event in summer 2015 with maximum temperatures of 27°C and 34°C, respectively. The results show that over 76% variation among different crops in SIF observations was explained by variation in vegetation biochemistry and structure. In addition, the changes of vegetation biochemistry and structure explained as much as 73% variation between the two days in far-red SIF, and 40% variation in red SIF. The remaining unexplained variation was mostly attributed to the variability in physiological status. We conclude that reflectance provides valuable information to account for biochemical and structural effects on SIF and to advance analysis of SIF observations. The combination of RTMs, reflectance and SIF opens new pathways to detect vegetation biochemical, structural and physiological changes.

Sun-induced chlorophyll fluorescence is more strongly related to absorbed light than to photosynthesis at half-hourly resolution in a rice paddy

Sun-induced chlorophyll fluorescence (SiF) is increasingly used as a proxy for vegetation canopy photosynthesis. While ground-based, airborne, and satellite observations have demonstrated a strong linear relationship between SiF and gross primary production (GPP) at seasonal scales, their relationships at high temporal resolution across diurnal to seasonal scales remain unclear. In this study, far-red canopy SiF, GPP, and absorbed photosynthetically active radiation (APAR) were continuously monitored using automated spectral systems and an eddy flux tower over an entire growing season in a rice paddy. At half-hourly resolution, strong linear relationships between SiF and GPP (R2 = 0.76) and APAR and GPP (R2 = 0.76) for the whole growing season were observed. We found that relative humidity, diffuse PAR fraction, and growth stage influenced the relationships between SiF and GPP, and APAR and GPP, and incorporating those factors into multiple regression analysis led to improvements up to R2 = 0.83 and R2 = 0.88, respectively. Relationships between LUEp (=GPP/APAR) and LUEf (=SiF/APAR) were inconsistent at half-hourly and weak at daily resolutions (R2 = 0.24). Both at diurnal and seasonal time scales with half-hourly resolution, we found considerably stronger linear relationships between SiF and APAR than between either SiF and GPP or APAR and GPP. Overall, our results indicate that for subdiurnal temporal resolution, canopy SiF in the rice paddy is above all a very good proxy for APAR at diurnal and seasonal time scales and that therefore SiF-based GPP estimation needs to take into account relevant environmental information to model LUEp. These findings can help develop mechanistic links between canopy SiF and GPP across multiple temporal scales.

Variability of sun-induced chlorophyll fluorescence according to stand age-related processes in a managed loblolly pine forest.

Leaf fluorescence can be used to track plant development and stress, and is considered the most direct measurement of photosynthetic activity available from remote sensing techniques. Red and far-red sun-induced chlorophyll fluorescence (SIF) maps were generated from high spatial resolution images collected with the HyPlant airborne spectrometer over even-aged loblolly pine plantations in North Carolina (United States). Canopy fluorescence yield (i.e., the fluorescence flux normalized by the light absorbed) in the red and far-red peaks was computed. This quantifies the fluorescence emission efficiencies that are more directly linked to canopy function compared to SIF radiances. Fluorescence fluxes and yields were investigated in relation to tree age to infer new insights on the potential of those measurements in better describing ecosystem processes. The results showed that red fluorescence yield varies with stand age. Young stands exhibited a nearly twofold higher red fluorescence yield than mature forest plantations, while the far-red fluorescence yield remained constant. We interpreted this finding in a context of photosynthetic stomatal limitation in aging loblolly pine stands. Current and future satellite missions provide global datasets of SIF at coarse spatial resolution, resulting in intrapixel mixture effects, which could be a confounding factor for fluorescence signal interpretation. To mitigate this effect, we propose a surrogate of the fluorescence yield, namely the Canopy Cover Fluorescence Index (CCFI) that accounts for the spatial variability in canopy structure by exploiting the vegetation fractional cover. It was found that spatial aggregation tended to mask the effective relationships, while the CCFI was still able to maintain this link. This study is a first attempt in interpreting the fluorescence variability in aging forest stands and it may open new perspectives in understanding long-term forest dynamics in response to future climatic conditions from remote sensing of SIF.

Linking canopy scattering of far-red sun-induced chlorophyll fluorescence with reflectance

Remotely sensed sun-induced chlorophyll fluorescence (SIF) has been used as an indicator of global terrestrial vegetation photosynthesis. The connection between SIF and photosynthesis allows its use for improving estimates of gross primary production (GPP) and monitoring plant stress. In these analyses, up-scaling of the relationship between SIF and photosynthesis from the photosynthetic level to the canopy, regional or global scale has been one of the main challenges. The scaling is strongly affected by the radiative transfer of emitted SIF, notably scattering and re-absorption of SIF. It is essential to understand these processes in order to differentiate effects of canopy structural variation from effects of photosynthesis functional variation on SIF. In this study, we derive the relationship between canopy scattering of SIF and top-of-canopy (TOC) reflectance analytically, by investigating the radiative transfer of incident light and emitted SIF. The similarity of radiative transfer of intercepted incident light and emitted SIF results in a simple relationship between reflectance and canopy scattering of SIF. In particular, we find that the ratio of far-red reflectance (R) to the product of canopy interceptance (i0) and leaf albedo (ω) is an accurate estimate of canopy scattering of far-red SIF (i.e., σFC=Ri0ω). SCOPE model simulations are used to validate our findings. The relationship we found provides an easy and accurate approach for rapid decoupling canopy structural and functional regulation of SIF, and correction of SIF for bidirectional effects. This will improve estimates of canopy photosynthesis from SIF.

Model-based analysis of the relationship between sun-induced chlorophyll fluorescence and gross primary production for remote sensing applications

Abstract Remote sensing of sun-induced chlorophyll fluorescence (SIF) is a novel optical tool for the assessment of terrestrial photosynthesis or gross primary production (GPP). Several recent studies have demonstrated the strong link between GPP and space-borne retrievals of SIF at broad scales. However, critical gaps remain between short-term small-scale mechanistic understanding and seasonal global observations. Here, we present a model-based analysis of the relationship between SIF and GPP across scales for diverse vegetation types and a range of meteorological conditions, with the ultimate focus on reproducing the environmental conditions during remote sensing measurements. The coupled fluorescence-photosynthesis model SCOPE is used to simulate GPP and SIF at the both leaf and canopy levels for 13 flux sites. Analyses were conducted to investigate the effects of temporal scaling, canopy structure, overpass time, and spectral domain on the relationship between SIF and GPP. The simulated SIF is highly non-linear with GPP at the leaf level and instantaneous time scale and tends to linearize when scaling to the canopy level and daily to seasonal. These relationships are consistent across a wide range of vegetation types. The relationship between SIF and GPP is primarily driven by absorbed photosynthetically active radiation (APAR), especially at the seasonal scale, although the photosynthetic efficiency also contributes to strengthen the link between them. The linearization of their relationship from leaf to canopy and averaging over time is because the overall conditions of the canopy fall within the range of the linear responses of GPP and SIF to light and the photosynthetic capacity. Our results further show that the top-of-canopy relationships between simulated SIF and GPP have similar linearity regardless of whether we used the morning or midday satellite overpass times. Field measurements confirmed these findings. In addition, the simulated red SIF at 685 nm has a similar relationship with GPP as that of far-red SIF at 740 nm at the canopy level. These findings provide model-based evidence to interpret remotely sensed SIF data and their relationship with GPP.