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Quantifying and Validating Remote Sensing Measurements of Chlorophyll Fluorescence

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A special issue of Remote Sensing (ISSN 2072-4292).

Deadline for manuscript submissions: closed (31 December 2018) | Viewed by 45268

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Dr. Elizabeth M. Middleton

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Guest Editor

NASA Goddard Space Flight Center, Greenbelt, MD, USA
Interests: remote sensing and in-situ measurements of plant stress; in-situ dynamic measurements of photosynthesis, leaf-level chlorophyll fluorescence, and canopy-level solar-induced fluorescence (SIF), and bidirectional reflectance properties; field systems for measurement and validation of dynamic fluorescence and reflectance vegetation properties; terrestrial ecosystem spectroscopy from space

Dr. Albert Porcar-Castell

E-Mail Website
Guest Editor

Optics of Photosynthesis Laboratory, University of Helsinki, Helsinki, Finland
Interests: long-term field measurements; multiscale fluorescence spectroscopy; mechanistics of ecophysiological remote sensing; process-based models of photosynthesis; multiscale field measurements; new methodologies and instrumentation

Dr. Christiaan Van der Tol

E-Mail Website
Guest Editor

Univerisity of Twente, Enschede, The Netherlands
Interests: vegetation remote sensing; Surface energy fluxes; Solar Induced Chlorophyll Fluorescence (SIF); Radiative transfer models; SCOPE model

Special Issue Information

Dear Colleagues,

Chlorophyll fluorescence is an important tool used to quantify plant stress and photosynthetic function, previously accomplished primarily in laboratory settings. At the canopy and ecosystem scale, the remote sensing of solar-induced (chlorophyll) fluorescence (SIF) has provided new insights into fluorescence dynamics across landscapes and plant types, as well as bringing new challenges. SIF is now being retrieved by various remote sensing methods from satellites, airborne sensors, and ground-based systems. The selection of the FLuorescence EXplorer (FLEX) as the next European Space Agency’s Explorer 8 mission, designed to optimize fluorescence measurements across the emission spectrum, has stimulated new research at all scales: the leaf, canopy, ecosystem, and global. It has also stimulated new physically- and process-based models to describe the radiative transfer processes and magnitudes related to the linked energy pathways for fluorescence, reflectance, and thermal vegetation properties. Research and application themes that require further attention in these fluorescence studies include atmospheric correction approaches and methods to quantify, and especially to validate, the remote sensing observations being acquired at all scales.

Papers are welcome that address: fluorescence retrieval methods; methods to quantify and to validate remotely acquired dynamic (diurnal and seasonal) fluorescence observations; improved understanding about the links between fluorescence and photochemistry; new datasets offered for community evaluations; and model simulations that provide new approaches and/or insights. Discouraged are papers primarily describing sensor systems or unvalidated, qualitative mapping observations.

The applications or technologies in your work should be novel and should bring new information to the understanding and importance of the remote sensing of fluorescence measurements.

Dr. Elizabeth M. Middleton
Dr. Albert Porcar-Castell
Dr. Christiaan van der Tol
Guest Editors

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Keywords

chlorophyll fluorescence from leaf to top of atmosphere: measurement protocols and standards
solar-induced fluorescence (SIF) retrieval methods and validation approaches
atmospheric correction approaches for SIF proximal and remote measurements
in-situ chlorophyll fluorescence to support validation of remotely sensed SIF
modeling chlorophyll fluorescence and SIF, linked to validation efforts
linking chlorophyll fluorescence to photochemistry (e.g., photosynthesis rates, effects of photosystems PSII and PSI)
remote sensing of vegetation properties and indices related to chlorophyll fluorescence (e.g., chlorophyll content carotenoid content, LAI, APAR, non-photochemical quenching, photochemical reflectance index- PRI)
validation approaches using quantitative statistical methods

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Published Papers (7 papers)

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Research

20 pages, 2872 KiB

Open AccessArticle

Leaf-Level Spectral Fluorescence Measurements: Comparing Methodologies for Broadleaves and Needles

by Paulina A. Rajewicz, Jon Atherton, Luis Alonso and Albert Porcar-Castell

Remote Sens. 2019, 11(5), 532; https://doi.org/10.3390/rs11050532 - 5 Mar 2019

Cited by 19 | Viewed by 5611

Abstract

Successful measurements of chlorophyll fluorescence (ChlF) spectral properties (typically in the wavelength range of 650–850 nm) across plant species, environmental conditions, and stress levels are a first step towards establishing a quantitative link between solar-induced chlorophyll fluorescence (SIF), which can only be measured at discrete ChlF spectral bands, and photosynthetic functionality. Despite its importance and significance, the various methodologies for the estimation of leaf-level ChlF spectral properties have not yet been compared, especially when applied to leaves with complex morphology, such as needles. Here we present, to the best of our knowledge, a first comparison of protocols for measuring leaf-level ChlF spectra: a custom-made system designed to measure ChlF spectra at ambient and 77 K temperatures (optical chamber, OC), the widely used FluoWat leaf clip (FW), and an integrating sphere setup (IS). We test the three methods under low-light conditions, across two broadleaf species and one needle-like species. For the conifer, we characterize the effect of needle arrangements: one needle, three needles, and needle mats with as little gap fraction as technically possible. We also introduce a simple baseline correction method to account for non-fluorescence-related contributions to spectral measurements. Baseline correction was found especially useful in recovering the spectra nearby the filter cut-off. Results show that the shape of the leaf-level ChlF spectra remained largely unaffected by the measurement methodology and geometry in OC and FW methods. Substantially smaller red/far-red ratios were observed in the IS method. The comparison of needle arrangements indicated that needle mats could be a practical solution to investigate temporal changes in ChlF spectra of needle-like leaves as they produced more reproducible results and higher signals. Full article

(This article belongs to the Special Issue Quantifying and Validating Remote Sensing Measurements of Chlorophyll Fluorescence)

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27 pages, 4090 KiB

Open AccessArticle

Diurnal and Seasonal Variations in Chlorophyll Fluorescence Associated with Photosynthesis at Leaf and Canopy Scales

by Petya K. E. Campbell, Karl F. Huemmrich, Elizabeth M. Middleton, Lauren A. Ward, Tommaso Julitta, Craig S. T. Daughtry, Andreas Burkart, Andrew L. Russ and William P. Kustas

Remote Sens. 2019, 11(5), 488; https://doi.org/10.3390/rs11050488 - 27 Feb 2019

Cited by 81 | Viewed by 9874

Abstract

There is a critical need for sensitive remote sensing approaches to monitor the parameters governing photosynthesis, at the temporal scales relevant to their natural dynamics. The photochemical reflectance index (PRI) and chlorophyll fluorescence (F) offer a strong potential for monitoring photosynthesis at local, regional, and global scales, however the relationships between photosynthesis and solar induced F (SIF) on diurnal and seasonal scales are not fully understood. This study examines how the fine spatial and temporal scale SIF observations relate to leaf level chlorophyll fluorescence metrics (i.e., PSII yield, YII and electron transport rate, ETR), canopy gross primary productivity (GPP), and PRI. The results contribute to enhancing the understanding of how SIF can be used to monitor canopy photosynthesis. This effort captured the seasonal and diurnal variation in GPP, reflectance, F, and SIF in the O₂A (SIF_A) and O₂B (SIF_B) atmospheric bands for corn (Zea mays L.) at a study site in Greenbelt, MD. Positive linear relationships of SIF to canopy GPP and to leaf ETR were documented, corroborating published reports. Our findings demonstrate that canopy SIF metrics are able to capture the dynamics in photosynthesis at both leaf and canopy levels, and show that the relationship between GPP and SIF metrics differs depending on the light conditions (i.e., above or below saturation level for photosynthesis). The sum of SIF_A and SIF_B (SIF_A+B), as well as the SIF_A+B yield, captured the dynamics in GPP and light use efficiency, suggesting the importance of including SIF_B in monitoring photosynthetic function. Further efforts are required to determine if these findings will scale successfully to airborne and satellite levels, and to document the effects of data uncertainties on the scaling. Full article

(This article belongs to the Special Issue Quantifying and Validating Remote Sensing Measurements of Chlorophyll Fluorescence)

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19 pages, 1010 KiB

Open AccessArticle

Relation between Changes in Photosynthetic Rate and Changes in Canopy Level Chlorophyll Fluorescence Generated by Light Excitation of Different Led Colours in Various Background Light

by Linnéa Ahlman, Daniel Bånkestad and Torsten Wik

Remote Sens. 2019, 11(4), 434; https://doi.org/10.3390/rs11040434 - 20 Feb 2019

Cited by 3 | Viewed by 5125

Abstract

Using light emitting diodes (LEDs) for greenhouse illumination enables the use of automatic control, since both light quality and quantity can be tuned. Potential candidate signals when using biological feedback for light optimisation are steady-state chlorophyll a fluorescence gains at 740 nm, defined as the difference in steady-state fluorescence at 740 nm divided by the difference in incident light quanta caused by (a small) excitation of different LED colours. In this study, experiments were conducted under various background light (quality and quantity) to evaluate if these fluorescence gains change relative to each other. The light regimes investigated were intensities in the range 160–1000

μ mol m^{- 2} s^{- 1}

, and a spectral distribution ranging from 50% to 100% red light. No significant changes in the mutual relation of the fluorescence gains for the investigated LED colours (400, 420, 450, 530, 630 and 660 nm), could be observed when the background light quality was changed. However, changes were noticed as function of light quantity. When passing the photosynthesis saturate intensity level, no further changes in the mutual fluorescence gains could be observed. Full article

(This article belongs to the Special Issue Quantifying and Validating Remote Sensing Measurements of Chlorophyll Fluorescence)

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22 pages, 4424 KiB

Open AccessArticle

Diurnal and Seasonal Solar Induced Chlorophyll Fluorescence and Photosynthesis in a Boreal Scots Pine Canopy

by Caroline J. Nichol, Guillaume Drolet, Albert Porcar-Castell, Tom Wade, Neus Sabater, Elizabeth M. Middleton, Chris MacLellan, Janne Levula, Ivan Mammarella, Timo Vesala and Jon Atherton

Remote Sens. 2019, 11(3), 273; https://doi.org/10.3390/rs11030273 - 30 Jan 2019

Cited by 37 | Viewed by 6608

Abstract

Solar induced chlorophyll fluorescence has been shown to be increasingly an useful proxy for the estimation of gross primary productivity (GPP), at a range of spatial scales. Here, we explore the seasonality in a continuous time series of canopy solar induced fluorescence (hereafter SiF) and its relation to canopy gross primary production (GPP), canopy light use efficiency (LUE), and direct estimates of leaf level photochemical efficiency in an evergreen canopy. SiF was calculated using infilling in two bands from the incoming and reflected radiance using a pair of Ocean Optics USB2000+ spectrometers operated in a dual field of view mode, sampling at a 30 min time step using custom written automated software, from early spring through until autumn in 2011. The optical system was mounted on a tower of 18 m height adjacent to an eddy covariance system, to observe a boreal forest ecosystem dominated by Scots pine. (Pinus sylvestris) A Walz MONITORING-PAM, multi fluorimeter system, was simultaneously mounted within the canopy adjacent to the footprint sampled by the optical system. Following correction of the SiF data for O₂ and structural effects, SiF, SiF yield, LUE, the photochemicsl reflectance index (PRI), and the normalized difference vegetation index (NDVI) exhibited a seasonal pattern that followed GPP sampled by the eddy covariance system. Due to the complexities of solar azimuth and zenith angle (SZA) over the season on the SiF signal, correlations between SiF, SiF yield, GPP, and LUE were assessed on SZA <50° and under strictly clear sky conditions. Correlations found, even under these screened scenarios, resulted around ~r² = 0.3. The diurnal responses of SiF, SiF yield, PAM estimates of effective quantum yield (ΔF/F_m′), and meteorological parameters demonstrated some agreement over the diurnal cycle. The challenges inherent in SiF retrievals in boreal evergreen ecosystems are discussed. Full article

(This article belongs to the Special Issue Quantifying and Validating Remote Sensing Measurements of Chlorophyll Fluorescence)

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20 pages, 7183 KiB

Open AccessArticle

Upscaling Solar-Induced Chlorophyll Fluorescence from an Instantaneous to Daily Scale Gives an Improved Estimation of the Gross Primary Productivity

by Jiaochan Hu, Liangyun Liu, Jian Guo, Shanshan Du and Xinjie Liu

Remote Sens. 2018, 10(10), 1663; https://doi.org/10.3390/rs10101663 - 21 Oct 2018

Cited by 41 | Viewed by 5537

Abstract

Solar-induced chlorophyll fluorescence (SIF) is closely linked to the photosynthesis of plants and has the potential to estimate gross primary production (GPP) at different temporal and spatial scales. However, remotely sensed SIF at a ground or space level is usually instantaneous, which cannot represent the daily total SIF. The temporal mismatch between instantaneous SIF (SIF_inst) and daily GPP (GPP_daily) impacts their correlation across space and time. Previous studies have upscaled SIF_inst to the daily scale based on the diurnal cycle in the cosine of the solar zenith angle (

\cos (SZA)

) to correct the effects of latitude and length of the day on the variations in the SIF-GPP correlation. However, the important effects of diurnal weather changes due to cloud and atmospheric scattering were not considered. In this study, we present a SIF upscaling method using photosynthetically active radiation (PAR) as a driving variable. First, a conversion factor (i.e., the ratio of the instantaneous PAR (PAR_inst) to daily PAR (PAR_daily)) was used to upscale in-situ SIF measurements from the instantaneous to daily scale. Then, the performance of the SIF upscaling method was evaluated under changing weather conditions and different latitudes using continuous tower-based measurements at two sites. The results prove that our PAR-based method can reduce not only latitude-dependent but also the weather-dependent variations in the SIF-GPP model. Specifically, the PAR-based method gave a more accurate prediction of diurnal and daily SIF (SIF_daily) than the

\cos (SZA)

-based method, with decreased relative root mean square error (RRMSE) values from 42.2% to 25.6% at half-hour intervals and from 25.4% to 13.3% at daily intervals. Moreover, the PAR-based upscaled SIF_daily had a stronger correlation with the daily absorbed PAR (APAR) than both the SIF_inst and

\cos (SZA)

-based upscaled SIF_daily, especially for cloudy days with a coefficient of determination (R²) that increased from approximately 0.5 to 0.8. Finally, the PAR-based SIF_daily was linked to GPP_daily and compared to the SIF_inst or

\cos (SZA)

-based SIF_daily. The results indicate that the SIF-GPP correlation can obviously be improved, with an increased R² from approximately 0.65 to 0.75. Our study confirms the importance of upscaling SIF from the instantaneous to daily scale when linking SIF with GPP and emphasizes the need to take diurnal weather changes into account for SIF temporal upscaling. Full article

(This article belongs to the Special Issue Quantifying and Validating Remote Sensing Measurements of Chlorophyll Fluorescence)

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29 pages, 6657 KiB

Open AccessArticle

Compensation of Oxygen Transmittance Effects for Proximal Sensing Retrieval of Canopy–Leaving Sun–Induced Chlorophyll Fluorescence

by Neus Sabater, Jorge Vicent, Luis Alonso, Jochem Verrelst, Elizabeth M. Middleton, Albert Porcar-Castell and José Moreno

Remote Sens. 2018, 10(10), 1551; https://doi.org/10.3390/rs10101551 - 26 Sep 2018

Cited by 44 | Viewed by 5657

Abstract

Estimates of Sun–Induced vegetation chlorophyll Fluorescence (SIF) using remote sensing techniques are commonly determined by exploiting solar and/or telluric absorption features. When SIF is retrieved in the strong oxygen (O

_{2}

) absorption features, atmospheric effects must always be compensated. Whereas correction of [...] Read more.

_{2}

) absorption features, atmospheric effects must always be compensated. Whereas correction of atmospheric effects is a standard airborne or satellite data processing step, there is no consensus regarding whether it is required for SIF proximal–sensing measurements nor what is the best strategy to be followed. Thus, by using simulated data, this work provides a comprehensive analysis about how atmospheric effects impact SIF estimations on proximal sensing, regarding: (1) the sensor height above the vegetated canopy; (2) the SIF retrieval technique used, e.g., Fraunhofer Line Discriminator (FLD) family or Spectral Fitting Methods (SFM); and (3) the instrument’s spectral resolution. We demonstrate that for proximal–sensing scenarios compensating for atmospheric effects by simply introducing the O

_{2}

transmittance function into the FLD or SFM formulations improves SIF estimations. However, these simplistic corrections still lead to inaccurate SIF estimations due to the multiplication of spectrally convolved atmospheric transfer functions with absorption features. Consequently, a more rigorous oxygen compensation strategy is proposed and assessed by following a classic airborne atmospheric correction scheme adapted to proximal sensing. This approach allows compensating for the O

_{2}

absorption effects and, at the same time, convolving the high spectral resolution data according to the corresponding Instrumental Spectral Response Function (ISRF) through the use of an atmospheric radiative transfer model. Finally, due to the key role of O

_{2}

absorption on the evaluated proximal–sensing SIF retrieval strategies, its dependency on surface pressure (p) and air temperature (T) was also assessed. As an example, we combined simulated spectral data with p and T measurements obtained for a one–year period in the Hyytiälä Forestry Field Station in Finland. Of importance hereby is that seasonal dynamics in terms of T and p, if not appropriately considered as part of the retrieval strategy, can result in erroneous SIF seasonal trends that mimic those of known dynamics for temperature–dependent physiological responses of vegetation. Full article

(This article belongs to the Special Issue Quantifying and Validating Remote Sensing Measurements of Chlorophyll Fluorescence)

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17 pages, 8413 KiB

Open AccessArticle

Diurnal Response of Sun-Induced Fluorescence and PRI to Water Stress in Maize Using a Near-Surface Remote Sensing Platform

by Shan Xu, Zhigang Liu, Liang Zhao, Huarong Zhao and Sanxue Ren

Remote Sens. 2018, 10(10), 1510; https://doi.org/10.3390/rs10101510 - 20 Sep 2018

Cited by 38 | Viewed by 5766

Abstract

Sun-induced Fluorescence (SIF) and Photochemical Reflectance Index (PRI) data were collected in the field over maize to study their diurnal responses to different water stresses at the canopy scale. An automated field spectroscopy system was used to obtain continuous and long-term measurements of maize canopy in four field plots with different irrigation treatments. This system collects visible to near-infrared spectra with a spectrometer, which provides a sub-nanometer spectral resolution in the spectral range of 480~850 nm. The red SIF (F_R) and far red SIF (F_FR) data were retrieved by Spectral Fitting Methods (SFM) in the

O_{2}

-A band and

O_{2}

-B band, respectively. In addition to PRI,

Δ PRI

values were derived from PRI by subtracting an early morning PRI value. Photosynthetic active radiation (PAR) data, the canopy fraction of absorbed PAR (fPAR), and the air/canopy temperature and photosystem II operating efficiency (YII) at the leaf scale were collected concurrently. In this paper, the diurnal dynamics of each parameter before and after watering at the jointing stage were compared. The results showed that (i) both F_R and F_FR decreased under water stress, but F_R always peaked at noon, and the peak of F_FR advanced with the increase in stress. Leaf folding and the increase in Non-photochemical Quenching (NPQ) are the main reasons for this trend. Leaf YII gradually decreased from 8:00 to 14:00 and then recovered. In drought, leaf YII was smaller and decreased more rapidly. Therefore, the fluorescence yield at both the leaf and canopy scale responded to water stress. (ii) As good indicators of changes in NPQ, diurnal PRI and

Δ PRI

data also showed specific decreases due to water stress.

Δ PRI

can eliminate the impact of canopy structure. Under water stress,

Δ PRI

decreased rapidly from 8:00 to 13:00, and the maximum range of this decrease was approximately 0.05. After 13:00, their values started to increase but could not recover to their morning level. (iii) Higher canopy-air temperature differences (

Δ T

) indicate that stomatal closure leads to an increase in leaf temperature, which maintains a higher state in the afternoon. In summary, to cope with water stress, both leaf folding and changes in physiology are activated. To monitor drought, SIF performs best around midday, and PRI is better after noon. Full article

(This article belongs to the Special Issue Quantifying and Validating Remote Sensing Measurements of Chlorophyll Fluorescence)

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