Potential of the TROPOspheric Monitoring Instrument (TROPOMI) onboard the Sentinel-5 Precursor for the monitoring of terrestrial chlorophyll fluorescence

Global monitoring of sun-induced chlorophyll fluorescence (SIF) is improving our knowledge about the photosynthetic functioning of terrestrial ecosystems. The feasibility of SIF retrievals from spaceborne atmospheric spectrometers has been demonstrated by a number of studies in the last years. In this work, we investigate the potential of the upcoming TROPOspheric Monitoring Instrument (TROPOMI) onboard the Sentinel-5 Precursor satellite mission for SIF retrieval. TROPOMI will sample the 675–775 nm spectral window with a spectral resolution of 0.5 nm and a pixel size of 7 km × 7 km. We use an extensive set of simulated TROPOMI data in order to assess the uncertainty of single SIF retrievals and subsequent spatio-temporal composites. Our results illustrate the enormous improvement in SIF monitoring achievable with TROPOMI with respect to comparable spectrometers currently in-flight, such as the Global Ozone Monitoring Experiment-2 (GOME-2) instrument. We find that TROPOMI can reduce global uncertainties in SIF mapping by more than a factor of 2 with respect to GOME-2, which comes together with an approximately 5-fold improvement in spatial sampling. Finally, we discuss the potential of TROPOMI to map other important vegetation parameters at a global scale with moderate spatial resolution and short revisit time. Those include leaf photosynthetic pigments and proxies for canopy structure, which will complement SIF retrievals for a self-contained description of vegetation condition and functioning

Quantitative estimation of vegetation traits and temporal dynamics using 3-D radiative transfer models, high-resolution hyperspectral images and satellite imagery

Large-scale monitoring of vegetation dynamics by remote sensing is key to detecting early signs of vegetation decline. Spectral-based indicators of phys-iological plant traits (PTs) have the potential to quantify variations in pho-tosynthetic pigments, chlorophyll fluorescence emission, and structural changes of vegetation as a function of stress. However, the specific response of PTs to disease-induced decline in heterogeneous canopies remains largely unknown, which is critical for the early detection of irreversible damage at different scales. Four specific objectives were defined in this research: i) to assess the feasibility of modelling the incidence and severity of Phytophthora cinnamomi and Xylella fastidiosa based on PTs and biophysical properties of vegetation; ii) to assess non-visual early indicators, iii) to retrieve PT using radiative transfer models (RTM), high-resolution imagery and satellite observations; and iv) to establish the basis for scaling up PTs at different spatial resolutions using RTM for their retrieval in different vegetation co-vers. This thesis integrates different approaches combining field data, air- and space-borne imagery, and physical and empirical models that allow the retrieval of indicators and the evaluation of each component’s contribution to understanding temporal variations of disease-induced symptoms in heter-ogeneous canopies. Furthermore, the effects associated with the understory are introduced, showing not only their impact but also providing a compre-hensive model to account for it. Consequently, a new methodology has been established to detect vegetation health processes and the influence of biotic and abiotic factors, considering different components of the canopy and their impact on the aggregated signal. It is expected that, using the presented methods, existing remote sensors and future developments, the ability to detect and assess vegetation health globally will have a substantial impact not only on socio-economic factors, but also on the preservation of our eco-system as a whole

Assessing the contribution of understory sun-induced chlorophyll fluorescence through 3-D radiative transfer modelling and field data

A major international effort has been made to monitor sun-induced chlorophyll fluorescence (SIF) from space as a proxy for the photosynthetic activity of terrestrial vegetation. However, the effect of spatial heterogeneity on the SIF retrievals from canopy radiance derived from images with medium and low spatial resolution remains uncharacterised. In images from forest and agricultural landscapes, the background comprises a mixture of soil and understory and can generate confounding effects that limit the interpretation of the SIF at the canopy level. This paper aims to improve the understanding of SIF from coarse spatial resolutions in heterogeneous canopies by considering the separated contribution of tree crowns, understory and background components, using a modified version of the FluorFLIGHT radiative transfer model (RTM). The new model is compared with others through the RAMI model intercomparison framework and is validated with airborne data. The airborne campaign includes high-resolution data collected over a tree-grass ecosystem with the HyPlant imaging spectrometer within the FLuorescence EXplorer (FLEX) preparatory missions. Field data measurements were collected from plots with a varying fraction of tree and understory vegetation cover. The relationship between airborne SIF calculated from pure tree crowns and aggregated pixels shows the effect of the understory at different resolutions. For a pixel size smaller than the mean crown size, the impact of the background was low (R2 > 0.99; NRMSE 0.2). This study demonstrates that using a 3D RTM model improves the calculation of SIF significantly (R2 = 0.83, RMSE = 0.03 mW m−2 sr−1 nm−1) when the specific contribution of the soil and understory layers are accounted for, in comparison with the SIF calculated from mixed pixels that considers only one layer as background (R2 = 0.4, RMSE = 0.28 mW m−2 sr−1 nm−1). These results demonstrate the need to account for the contribution of SIF emitted by the understory in the quantification of SIF within tree crowns and within the canopy from aggregated pixels in heterogeneous forest canopies

Systematic Orbital Geometry-Dependent Variations in Satellite Solar-Induced Fluorescence (SIF) Retrievals

While solar-induced fluorescence (SIF) shows promise as a remotely-sensed measurement directly related to photosynthesis, interpretation and validation of satellite-based SIF retrievals remains a challenge. SIF is influenced by the fraction of absorbed photosynthetically-active radiation at the canopy level that depends upon illumination geometry as well as the escape of SIF through the canopy that depends upon the viewing geometry. Several approaches to estimate the effects of sun-sensor geometry on satellite-based SIF have been proposed, and some have been implemented, most relying upon satellite reflectance measurements and/or other ancillary data sets. These approaches, designed to ultimately estimate intrinsic or physiological components of SIF related to photosynthesis, have not generally been applied globally to satellite measurements. Here, we examine in detail how SIF and related reflectance-based indices from wide swath polar orbiting satellites in low Earth orbit vary systematically due to the host satellite orbital characteristics. We compare SIF and reflectance-based parameters from the Global Ozone Mapping Experiment 2 (GOME-2) on the MetOp-B platform and from the TROPOspheric Monitoring Instrument (TROPOMI) on the Sentinel 5 Precursor satellite with a focus on high northern latitudes in summer where observations at similar geometries and local times occur. We show that GOME-2 and TROPOMI SIF observations agree nearly to within estimated uncertainties when they are compared at similar observing geometries. We show that the cross-track dependence of SIF normalized by PAR and related reflectance-based indices are highly correlated for dense canopies, but diverge substantially as the vegetation within a field-of-view becomes more sparse. This has implications for approaches that utilize reflectance measurements to help account for SIF geometrical dependences in satellite measurements. To further help interpret the GOME-2 and TROPOMI SIF observations, we simulated cross-track dependences of PAR normalized SIF and reflectance-based indices with the one dimensional Soil-Canopy Observation Photosynthesis and Energy fluxes (SCOPE) canopy radiative transfer model at sun–satellite geometries that occur across the wide swaths of these instruments and examine the geometrical dependencies of the various components (e.g., fraction of absorbed PAR, SIF yield, and escape of SIF from the canopy) of the observed SIF signal. The simulations show that most of the cross-track variations in SIF result from the escape of SIF through the scattering canopy and not the illumination

New Methods for Measurements of Photosynthesis from Space

Our ability to close the Earth's carbon budget and predict feedbacks in a warming climate depends critically on knowing where, when, and how carbon dioxide (CO2) is exchanged between the land and atmosphere. In particular, determining the rate of carbon fixation by the Earth's biosphere (commonly referred to as gross primary productivity, or GPP) and the dependence of this productivity on climate is a central goal. Historically, GPP has been inferred from spectral imagery of the land and ocean. Assessment of GPP from the color of the land and ocean requires, however, additional knowledge of the types of plants in the scene, their regulatory mechanisms, and climate variables such as soil moisture—just the independent variables of interest! Sunlight absorbed by chlorophyll in photosynthetic organisms is mostly used to drive photosynthesis, but some can also be dissipated as heat or re‐radiated at longer wavelengths (660–800 nm). This near‐infrared light re‐emitted from illuminated plants is termed solarinduced fluorescence (SIF), and it has been found to strongly correlate with GPP. To advance our understanding of SIF and its relation to GPP and environmental stress at the planetary scale, the Keck Institute for Space Studies (KISS) convened a workshop—held in Pasadena, California, in August 2012—to focus on a newly developed capacity to monitor chlorophyll fluorescence from terrestrial vegetation by satellite. This revolutionary approach for retrieving global observations of SIF promises to provide direct and spatially resolved information on GPP, an ideal bottom‐up complement to the atmospheric net CO2 exchange inversions. Workshop participants leveraged our efforts on previous studies and workshops related to the European Space Agency’s FLuorescence EXplorer (FLEX) mission concept, which had already targeted SIF for a possible satellite mission and had developed a vibrant research community with many important publications. These studies, mostly focused on landscape, canopy, and leaf‐level interpretation, provided the ground‐work for the workshop, which focused on the global carbon cycle and synergies with atmospheric net flux inversions. Workshop participants included key members of several communities: plant physiologists with experience using active fluorescence methods to quantify photosynthesis; ecologists and radiative transfer experts who are studying the challenge of scaling from the leaf to regional scales; atmospheric scientists with experience retrieving photometric information from space‐borne spectrometers; and carbon cycle experts who are integrating new observations into models that describe the exchange of carbon between the atmosphere, land and ocean. Together, the participants examined the link between “passive” fluorescence observed from orbiting spacecraft and the underlying photochemistry, plant physiology and biogeochemistry of the land and ocean. This report details the opportunity for forging a deep connection between scientists doing basic research in photosynthetic mechanisms and the more applied community doing research on the Earth System. Too often these connections have gotten lost in empiricism associated with the coarse scale of global models. Chlorophyll fluorescence has been a major tool for basic research in photosynthesis for nearly a century. SIF observations from space, although sensing a large footprint, probe molecular events occurring in the leaves below. This offers an opportunity for direct mechanistic insight that is unparalleled for studies of biology in the Earth System. A major focus of the workshop was to review the basic mechanisms that underlie this phenomenon, and to explore modeling tools that have been developed to link the biophysical and biochemical knowledge of photosynthesis with the observable—in this case, the radiance of SIF—seen by the satellite. Discussions led to the identification of areas where knowledge is still lacking. For example, the inability to do controlled illumination observations from space limits the ability to fully constrain the variables that link fluorescence and photosynthesis. Another focus of the workshop explored a “top‐down” view of the SIF signal from space. Early studies clearly identified a strong correlation between the strength of this signal and our best estimate of the rate of photosynthesis (GPP) over the globe. New studies show that this observation provides improvements over conventional reflectance‐based remote sensing in detecting seasonal and environmental (particularly drought related) modulation of photosynthesis. Apparently SIF responds much more quickly and with greater dynamic range than typical greenness indices when GPP is perturbed. However, discussions at the workshop also identified areas where top‐down analysis seemed to be “out in front” of mechanistic studies. For example, changes in SIF based on changes in canopy light interception and the light use efficiency of the canopy, both of which occur in response to drought, are assumed equivalent in the top‐down analysis, but the mechanistic justification for this is still lacking from the bottom‐up side. Workshop participants considered implications of these mechanistic and empirical insights for large‐scale models of the carbon cycle and biogeochemistry, and also made progress toward incorporating SIF as a simulated output in land surface models used in global and regional‐scale analysis of the carbon cycle. Comparison of remotely sensed SIF with modelsimulated SIF may open new possibilities for model evaluation and data assimilation, perhaps leading to better modeling tools for analysis of the other retrieval from GOSAT satellite, atmospheric CO2 concentration. Participants also identified another application for SIF: a linkage to the physical climate system arising from the ability to better identify regional development of plant water stress. Decreases in transpiration over large areas of a continent are implicated in the development and “locking‐in” of drought conditions. These discussions also identified areas where current land surface models need to be improved in order to enable this research. Specifically, the radiation transport treatments need dramatic overhauls to correctly simulate SIF. Finally, workshop participants explored approaches for retrieval of SIF from satellite and ground‐based sensors. The difficulty of resolving SIF from the overwhelming flux of reflected sunlight in the spectral region where fluorescence occurs was once a major impediment to making this measurement. Placement of very high spectral resolution spectrometers on GOSAT (and other greenhouse gas–sensing satellites) has enabled retrievals based on infilling of solar Fraunhofer lines, enabling accurate fluorescence measurements even in the presence of moderately thick clouds. Perhaps the most interesting challenge here is that there is no readily portable ground‐based instrumentation that even approaches the capability of GOSAT and other planned greenhouse gas satellites. This strongly limits scientists’ ability to conduct ground‐based studies to characterize the footprint of the GOSAT measurement and to conduct studies of radiation transport needed to interpret SIF measurement. The workshop results represent a snapshot of the state of knowledge in this area. New research activities have sprung from the deliberations during the workshop, with publications to follow. The introduction of this new measurement technology to a wide slice of the community of Earth System Scientists will help them understand how this new technology could help solve problems in their research, address concerns about the interpretation, identify future research needs, and elicit support of the wider community for research needed to support this observation. Somewhat analogous to the original discovery that vegetation indices could be derived from satellite measurements originally intended to detect clouds, the GOSAT observations are a rare case in which a (fortuitous) global satellite dataset becomes available before the research community had a consolidated understanding on how (beyond an empirical correlation) it could be applied to understanding the underlying processes. Vegetation indices have since changed the way we see the global biosphere, and the workshop participants envision that fluorescence can perform the next indispensable step by complementing these measurements with independent estimates that are more indicative of actual (as opposed to potential) photosynthesis. Apart from the potential FLEX mission, no dedicated satellite missions are currently planned. OCO‐2 and ‐3 will provide much more data than GOSAT, but will still not allow for regional studies due to the lack of mapping capabilities. Geostationary observations may even prove most useful, as they could track fluorescence over the course of the day and clearly identify stress‐related down‐regulation of photosynthesis. Retrieval of fluorescence on the global scale should be recognized as a valuable tool; it can bring the same quantum leap in our understanding of the global carbon cycle as vegetation indices once did

Chlorophyll a fluorescence illuminates a path connecting plant molecular biology to Earth-system science

Remote sensing methods enable detection of solar-induced chlorophyll a fluorescence. However, to unleash the full potential of this signal, intensive cross-disciplinary work is required to harmonize biophysical and ecophysiological studies. For decades, the dynamic nature of chlorophyll a fluorescence (ChlaF) has provided insight into the biophysics and ecophysiology of the light reactions of photosynthesis from the subcellular to leaf scales. Recent advances in remote sensing methods enable detection of ChlaF induced by sunlight across a range of larger scales, from using instruments mounted on towers above plant canopies to Earth-orbiting satellites. This signal is referred to as solar-induced fluorescence (SIF) and its application promises to overcome spatial constraints on studies of photosynthesis, opening new research directions and opportunities in ecology, ecophysiology, biogeochemistry, agriculture and forestry. However, to unleash the full potential of SIF, intensive cross-disciplinary work is required to harmonize these new advances with the rich history of biophysical and ecophysiological studies of ChlaF, fostering the development of next-generation plant physiological and Earth-system models. Here, we introduce the scale-dependent link between SIF and photosynthesis, with an emphasis on seven remaining scientific challenges, and present a roadmap to facilitate future collaborative research towards new applications of SIF.Peer reviewe

Surface and Temporal Biosignatures

Recent discoveries of potentially habitable exoplanets have ignited the prospect of spectroscopic investigations of exoplanet surfaces and atmospheres for signs of life. This chapter provides an overview of potential surface and temporal exoplanet biosignatures, reviewing Earth analogues and proposed applications based on observations and models. The vegetation red-edge (VRE) remains the most well-studied surface biosignature. Extensions of the VRE, spectral "edges" produced in part by photosynthetic or nonphotosynthetic pigments, may likewise present potential evidence of life. Polarization signatures have the capacity to discriminate between biotic and abiotic "edge" features in the face of false positives from band-gap generating material. Temporal biosignatures -- modulations in measurable quantities such as gas abundances (e.g., CO2), surface features, or emission of light (e.g., fluorescence, bioluminescence) that can be directly linked to the actions of a biosphere -- are in general less well studied than surface or gaseous biosignatures. However, remote observations of Earth's biosphere nonetheless provide proofs of concept for these techniques and are reviewed here. Surface and temporal biosignatures provide complementary information to gaseous biosignatures, and while likely more challenging to observe, would contribute information inaccessible from study of the time-averaged atmospheric composition alone.Comment: 26 pages, 9 figures, review to appear in Handbook of Exoplanets. Fixed figure conversion error