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

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

Drone Measurements of Solar-Induced Chlorophyll Fluorescence Acquired with a Low-Weight DFOV Spectrometer System

Solar induced chlorophyll fluorescence (SIF) emitted from plant canopies is now retrievable from space. In addition, SIF is now also routinely measured from fixed tower platforms. However there is a scale gap between temporally continuous tower measurements and spatially coarse satellite retrievals that is now being bridged by drone technology. Drone retrievals of SIF can be used to help unravel the structural and species component dependencies that occur across space on the scale of meters in heterogeneous vegetation types. Also when flown at sufficient altitude, drones can be used to simulate, and potentially validate satellite retrievals of SIF. We flew a dual field of view spectrometer system, the Piccolo doppio, above a boreal forest with the aim of retrieving SIF. Our flights were designed to assess both spatial heterogeneity of SIF driven by changes in vegetation cover type and to simulate satellite pixels by flying at a relatively high altitude.Peer reviewe

Onset of photosynthesis in spring speeds up monoterpene synthesis and leads to emission bursts

Emissions of biogenic volatile organic compounds (BVOC) by boreal evergreen trees have strong seasonality, with low emission rates during photosynthetically inactive winter and increasing rates towards summer. Yet, the regulation of this seasonality remains unclear. We measured in situ monoterpene emissions from Scots pine shoots during several spring periods and analysed their dynamics in connection with the spring recovery of photosynthesis. We found high emission peaks caused by enhanced monoterpene synthesis consistently during every spring period (monoterpene emission bursts, MEB). The timing of the MEBs varied relatively little between the spring periods. The timing of the MEBs showed good agreement with the photosynthetic spring recovery, which was studied with simultaneous measurements of chlorophyll fluorescence, CO2 exchange and a simple, temperature history-based proxy for state of photosynthetic acclimation, S. We conclude that the MEBs were related to the early stages of photosynthetic recovery, when the efficiency of photosynthetic carbon reactions is still low whereas the light harvesting machinery actively absorbs light energy. This suggests that the MEBs may serve a protective functional role for the foliage during this critical transitory state and that these high emission peaks may contribute to atmospheric chemistry in the boreal forest in springtime. Emissions of biogenic volatile organic compounds (BVOC) by boreal evergreen trees have strong seasonality. We measured high emission peaks from Scots pine shoots caused by enhanced monoterpene synthesis taking place simultaneously with the photosynthetic spring recovery. We conclude that the increased emissions were related to the photosynthetic recovery, when the efficiency of photosynthetic carbon reactions is low whereas the light harvesting machinery actively absorbs light energy. Increased emissions may serve a protective functional role for the foliage during the transitory state, and these high emission peaks may contribute to atmospheric chemistry in the boreal forest in springtime.Peer reviewe

Improving Estimates of Gross Primary Productivity by Assimilating Solar-Induced Fluorescence Satellite Retrievals in a Terrestrial Biosphere Model Using a Process-Based SIF Model

Abstract Over the last few years, solar-induced chlorophyll fluorescence (SIF) observations from space have emerged as a promising resource for evaluating the spatio-temporal distribution of gross primary productivity (GPP) simulated by global terrestrial biosphere models. SIF can be used to improve GPP simulations by optimizing critical model parameters through statistical Bayesian data assimilation techniques. A prerequisite is the availability of a functional link between GPP and SIF in terrestrial biosphere models. Here we present the development of a mechanistic SIF observation operator in the ORCHIDEE (Organizing Carbon and Hydrology In Dynamic Ecosystems) terrestrial biosphere model. It simulates the regulation of photosystem II fluorescence quantum yield at the leaf level thanks to a novel parameterization of non-photochemical quenching as a function of temperature, photosynthetically active radiation, and normalized quantum yield of photochemistry. It emulates the radiative transfer of chlorophyll fluorescence to the top of the canopy using a parametric simplification of the SCOPE (Soil Canopy Observation Photosynthesis Energy) model. We assimilate two years of monthly OCO-2 (Orbiting Carbon Observatory-2) SIF product at 0.5° (2015?2016) to optimize ORCHIDEE photosynthesis and phenological parameters over an ensemble of grid points for all plant functional types. The impact on the simulated GPP is considerable with a large decrease of the global scale budget by 28 GtC/year over the period 1990?2009. The optimized GPP budget (134/136 GtC/year over 1990?2009/2001?2009) remarkably agrees with independent GPP estimates, FLUXSAT (137 GtC/year over 2001?2009) in particular and FLUXCOM (121 GtC/year over 1990?2009). Our results also suggest a biome dependency of the SIF-GPP relationship that needs to be improved for some plant functional types.Peer reviewe

OCO-2 advances photosynthesis observation from space via solar-induced chlorophyll fluorescence

Quantifying gross primary production (GPP) remains a major challenge in global carbon cycle research. Spaceborne monitoring of solar-induced chlorophyll fluorescence (SIF), an integrative photosynthetic signal of molecular origin, can assist in terrestrial GPP monitoring. However, the extent to which SIF tracks spatiotemporal variations in GPP remains unresolved. Orbiting Carbon Observatory-2 (OCO-2)’s SIF data acquisition and fine spatial resolution permit direct validation against ground and airborne observations. Empirical orthogonal function analysis shows consistent spatiotemporal correspondence between OCO-2 SIF and GPP globally. A linear SIF-GPP relationship is also obtained at eddy-flux sites covering diverse biomes, setting the stage for future investigations of the robustness of such a relationship across more biomes. Our findings support the central importance of high-quality satellite SIF for studying terrestrial carbon cycle dynamics

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

EUROSPEC : at the interface between remote-sensing and ecosystem CO2 flux measurements in Europe

Resolving the spatial and temporal dynamics of gross primary productivity (GPP) of terrestrial ecosystems across different scales remains a challenge. Remote sensing is regarded as the solution to upscale point observations conducted at the ecosystem level, using the eddy covariance (EC) technique, to the landscape and global levels. In addition to traditional vegetation indices, the photochemical reflectance index (PRI) and the emission of solar-induced chlorophyll fluorescence (SIF), now measurable from space, provide a new range of opportunities to monitor the global carbon cycle using remote sensing. However, the scale mismatch between EC observations and the much coarser satellite-derived data complicate the integration of the two sources of data. The solution is to establish a network of in situ spectral measurements that can act as a bridge between EC measurements and remote-sensing data. In situ spectral measurements have already been conducted for many years at EC sites, but using variable instrumentation, setups, and measurement standards. In Europe in particular, in situ spectral measurements remain highly heterogeneous. The goal of EUROSPEC Cost Action ES0930 was to promote the development of common measuring protocols and new instruments towards establishing best practices and standardization of these measurements. In this review we describe the background and main tradeoffs of in situ spectral measurements, review the main results of EUROSPEC Cost Action, and discuss the future challenges and opportunities of in situ spectral measurements for improved estimation of local and global estimates of GPP over terrestrial ecosystems.Peer reviewe

The handbook for standardized field and laboratory measurements in terrestrial climate change experiments and observational studies (ClimEx)

Climate change is a world-wide threat to biodiversity and ecosystem structure, functioning and services. To understand the underlying drivers and mechanisms, and to predict the consequences for nature and people, we urgently need better understanding of the direction and magnitude of climate change impacts across the soil-plant-atmosphere continuum. An increasing number of climate change studies are creating new opportunities for meaningful and high-quality generalizations and improved process understanding. However, significant challenges exist related to data availability and/or compatibility across studies, compromising opportunities for data re-use, synthesis and upscaling. Many of these challenges relate to a lack of an established 'best practice' for measuring key impacts and responses. This restrains our current understanding of complex processes and mechanisms in terrestrial ecosystems related to climate change. To overcome these challenges, we collected best-practice methods emerging from major ecological research networks and experiments, as synthesized by 115 experts from across a wide range of scientific disciplines. Our handbook contains guidance on the selection of response variables for different purposes, protocols for standardized measurements of 66 such response variables and advice on data management. Specifically, we recommend a minimum subset of variables that should be collected in all climate change studies to allow data re-use and synthesis, and give guidance on additional variables critical for different types of synthesis and upscaling. The goal of this community effort is to facilitate awareness of the importance and broader application of standardized methods to promote data re-use, availability, compatibility and transparency. We envision improved research practices that will increase returns on investments in individual research projects, facilitate second-order research outputs and create opportunities for collaboration across scientific communities. Ultimately, this should significantly improve the quality and impact of the science, which is required to fulfil society's needs in a changing world.Peer reviewe

OCO-2 advances photosynthesis observation from space via solar-induced chlorophyll fluorescence

Quantifying gross primary production (GPP) remains a major challenge in global carbon cycle research. Spaceborne monitoring of solar-induced chlorophyll fluorescence (SIF), an integrative photosynthetic signal of molecular origin, can assist in terrestrial GPP monitoring. However, the extent to which SIF tracks spatiotemporal variations in GPP remains unresolved. Orbiting Carbon Observatory-2 (OCO-2)’s SIF data acquisition and fine spatial resolution permit direct validation against ground and airborne observations. Empirical orthogonal function analysis shows consistent spatiotemporal correspondence between OCO-2 SIF and GPP globally. A linear SIF-GPP relationship is also obtained at eddy-flux sites covering diverse biomes, setting the stage for future investigations of the robustness of such a relationship across more biomes. Our findings support the central importance of high-quality satellite SIF for studying terrestrial carbon cycle dynamics

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