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Sun-induced fluorescence (SIF) retrieved from satellite measurements has been widely used as proxy for chlorophyll-a concentration and as indicator of phytoplankton physiological status in oceans. The practical use of this naturally occurring light signal in environmental research is, however, under-exploited, particularly in research focusing on optically complex waters such as inland and coastal waters. In this study, we investigated methodological and knowledge gaps in remote sensing of chlorophyll-a SIF in optically complex waters by reviewing the theory behind SIF occurrence, the availability of existing and upcoming instrumentation, the availability of SIF retrieval schemes, and the applications for aquatic research. Starting with an overview of factors that influence SIF leaving the water body, we further investigated available and upcoming observational capacity by in situ, airborne and satellite sensors. We discuss requirements for spatial, spectral, temporal, and radiometric resolution of observing systems in the context of SIF dynamics. We assessed viable retrieval techniques able to disentangle SIF from non-SIF contribution to the upwelling radiance, ranging from the established multispectral Fluorescence Line Height algorithm (FLH) approach to hyperspectral approaches including model inversion, spectral fitting methods and machine learning regression procedures. Finally, we provide an overview of applications, which could potentially benefit from improved SIF emission estimates such as biomass estimation, algal bloom investigation and primary productivity modelling.

Remote sensing of solar-induced chlorophyll fluorescence (SIF) is a rapidly advancing front in terrestrial vegetation science, with emerging capability in space-based methodologies and diverse application prospects. Although remote sensing of SIF – especially from space – is seen as a contemporary new specialty for terrestrial plants, it is founded upon a multi-decadal history of research, applications, and sensor developments in active and passive sensing of chlorophyll fluorescence. Current technical capabilities allow SIF to be measured across a range of biological, spatial, and temporal scales. As an optical signal, SIF may be assessed remotely using high-resolution spectral sensors in tandem with state-of-the-art algorithms to distinguish the emission from reflected and/or scattered ambient light. Because the red to far-red SIF emission is detectable non-invasively, it may be sampled repeatedly to acquire spatio-temporally explicit information about photosynthetic light responses and steady-state behaviour in vegetation. Progress in this field is accelerating with innovative sensor developments, retrieval methods, and modelling advances. This review distills the historical and current developments spanning the last several decades. It highlights SIF heritage and complementarity within the broader field of fluorescence science, the maturation of physiological and radiative transfer modelling, SIF signal retrieval strategies, techniques for field and airborne sensing, advances in satellite-based systems, and applications of these capabilities in evaluation of photosynthesis and stress effects. Progress, challenges, and future directions are considered for this unique avenue of remote sensing.

The Fluorescence Explorer (FLEX) mission has been recently selected as the 8th Earth Explorer by the European Space Agency (ESA). It will be the first mission specifically designed to measure from space vegetation fluorescence emission, by making use of very high spectral resolution imaging spectroscopy techniques. Vegetation fluorescence is the best proxy to actual vegetation photosynthesis which can be measurable from space, allowing an improved quantification of vegetation carbon assimilation and vegetation stress conditions, thus having key relevance for global mapping of ecosystems dynamics and aspects related with agricultural production and food security. The FLEX mission carries the FLORIS spectrometer, with a spectral resolution in the range of 0.3 nm, and is designed to fly in tandem with Copernicus Sentinel-3, in order to provide all the necessary spectral / angular information to disentangle emitted fluorescence from reflected radiance, and to allow proper interpretation of the observed fluorescence spatial and temporal dynamics.

In November 2015, the FLuorescence EXplorer (FLEX) was selected as the eighth Earth Explorer mission of the European Space Agency. The tandem mission concept will provide measurements at a spectral and spatial resolution enabling the retrieval and interpretation of the full chlorophyll fluorescence spectrum emitted by the terrestrial vegetation. This paper provides a mission concept overview of the scientific goals, the key objectives related to fluorescence, and the requirements guaranteeing the fitness for purpose of the resulting scientific data set. We present the mission design at the time of selection, i.e., at the end of project phase Phase A/B1, as developed by two independent industrial consortia. The mission concepts both rely on a single payload Fluorescence Imaging Spectrometer, covering the spectral range from 500 to 780 nm. In the oxygen absorption bands, its spectral resolution will be 0.3 nm with a spectral sampling interval of 0.1 nm. The swath width of the spectrometer is 150 km and the spatial resolution will be 300 × 300 m-2 . The satellite will fly in tandem with Sentinel-3 providing different and complementary measurements with a temporal collocation of 6 to 15 s. The FLEX launch is scheduled for 2022.

Remote estimation of Sun-induced chlorophyll fluorescence emitted by terrestrial vegetation can provide an unparalleled opportunity to track spatiotemporal variations of photosynthetic efficiency. Here we provide the first direct experimental evidence that the two peaks of the chlorophyll fluorescence spectrum can be accurately mapped from high-resolution radiance spectra and that the signal is linked to variations in actual photosynthetic efficiency. Red and far red fluorescence measured using a novel airborne imaging spectrometer over a grass carpet treated with an herbicide known to inhibit photosynthesis was significantly higher than the corresponding signal from an equivalent untreated grass carpet. The reflectance signal of the two grass carpets was indistinguishable, confirming that the fast dynamic changes in fluorescence emission were related to variations in the functional status of actual photosynthesis induced by herbicide application. Our results from a controlled experiment at the local scale illustrate the potential for the global mapping of terrestrial photosynthesis through space-borne measurements of chlorophyll fluorescence. Key Points A novel high-resolution airborne sensor is flown Both red and far red Sun-induced fluorescence signals are accurately quantified Red and far red fluorescence tracks variations in photosynthetic efficiency

Remote estimation of Sun-induced chlorophyll fluorescence emitted by terrestrial vegetation can provide an unparalleled opportunity to track spatiotemporal variations of photosynthetic efficiency. Here we provide the first direct experimental evidence that the two peaks of the chlorophyll fluorescence spectrum can be accurately mapped from high-resolution radiance spectra and that the signal is linked to variations in actual photosynthetic efficiency. Red and far red fluorescence measured using a novel airborne imaging spectrometer over a grass carpet treated with an herbicide known to inhibit photosynthesis was significantly higher than the corresponding signal from an equivalent untreated grass carpet. The reflectance signal of the two grass carpets was indistinguishable, confirming that the fast dynamic changes in fluorescence emission were related to variations in the functional status of actual photosynthesis induced by herbicide application. Our results from a controlled experiment at the local scale illustrate the potential for the global mapping of terrestrial photosynthesis through space-borne measurements of chlorophyll fluorescence.

Computational modeling in biology requires sophisticated software tools. Precise communication and effective sharing of the models developed by researchers requires standard formats for storing, annotating, and exchanging models between software systems. Developing such standards is the driving vision behind the Systems Biology Markup Language (SBML) and several related efforts that we discuss in this chapter. At the same time, such standards are only enablers and ideally should be hidden “under the hood” of modeling environments that provide users with high-level, flexible facilities for working with computational models. As an example of the modern software systems available today, we discuss the Virtual Cell and illustrate its support for typical modeling activities in biology.

State-of-the-art optical remote sensing of vegetation canopies is reviewed here to stimulate support from laboratory and field plant research. This overview of recent satellite spectral sensors and the methods used to retrieve remotely quantitative biophysical and biochemical characteristics of vegetation canopies shows that there have been substantial advances in optical remote sensing over the past few decades. Nevertheless, adaptation and transfer of currently available fluorometric methods aboard air- and space-borne platforms can help to eliminate errors and uncertainties in recent remote sensing data interpretation. With this perspective, red and blue-green fluorescence emission as measured in the laboratory and field is reviewed. Remotely sensed plant fluorescence signals have the potential to facilitate a better understanding of vegetation photosynthetic dynamics and primary production on a large scale. The review summarizes several scientific challenges that still need to be resolved to achieve operational fluorescence based remote sensing approaches.

The application of hole burning spectroscopy (HB) in the study of photosynthetic systems offers an independent method for determining excited state lifetimes of particular chromophores. The rate constants of excitation energy transfer (EET) in photosynthetic antennae can be directly determined by time resolved fluorescence spectroscopy. For most bacterial and higher plants antennae is of the order of 10 to the -12 power/s. Efficient EET in pigment-protein complexes causes significant shortening (three orders of magnitude) of the excited state lifetimes T sub 1 in comparison with isolated pigments. The hole widths obtained in hole burning spectroscopy are proportional to the total relaxation time T sub 2: 1/T sub 2 = 1/2T sub 1 + 1/T sub 2*. In the presence of fast EET the T sub 1 contribution is dominant. The aim of this report is to compare the role of protein environment and efficiency of EET in photosystem II (PS II) core antenna chlorophyll protein complex (CPa2) in polyacrylamid gel with that of the core antenna in native PS II particles in buffer/glycerol glass (PS II part.).