Supplementary information 1 (S1): retrieval of remotely measured sun-induced chlorophyll fluorescence Fluorescence measurement of large ecosystems relies on passive measurements of sun-induced fluorescence. The approach uses Fraunhofer lines and atmospheric absorption lines, which reduce the incoming solar radiation reaching the Earth surface. In the spectral region of fluorescence emission, two main absorption bands that are due to the oxygen absorption by the earth atmosphere exist: 687 nm (O2B) and 760 nm (O2-A). Chlorophyll fluorescence emitted from the canopy occurs in these absorption bands and can be quantified with an enhanced signal-to-background ratio because of the greatly reduced reflectance. The Fraunhofer Line Discrimination method (FLD) had been proposed 40 years ago (1) and since then has been refined and used in various studies to retrieve fluorescence emission from natural vegetation (see (2) for review). Taking the advantages and disadvantages of the different approaches into account and considering several sensitivity studies, the 3FLD method proposed by Maier et al. (3) provides a good compromise between low complexity and stability for ground and airborne applications. However, this method needs the hyperspectral reflectance measurement of non-fluorescing surfaces, such as large, isolated fields of bare soil. Radiance measurements from the non-reflecting surface are compared with radiance measurements of the fluorescing canopy. Fluorescence can then be calculated according to eq. (S1) = − ∙ 1− (eq. S1) with I being the incoming radiance, L is the radiance of vegetation, and the subscripts “in” and “out” indicate the wavelengths within and outside of the absorption line, respectively (see also Fig. S1). The 3FLD method allows reliable detection in ground and airborne data as long as non-vegetated surfaces are present. However, for satellite applications and for a general use, also in densely vegetated areas, a physically based retrieval procedure is under development and will use a spectral un-mixing of the full high-resolution reflectance signature around solar and atmospheric absorption lines to quantify the shape and intensity of the two-peak fluorescence signal. Such a retrieval method is currently being developed within the framework of an ESA activity (4), and the first results look very promising and will be published elsewhere. Fig. S1: Principle of retrieval of sun-induced fluorescence in the atmospheric absorption lines, where I is incoming radiance and L is reflected, i.e. outgoing radiance, the subscripts “in” and “out” refer to radiance inside and outside of the atmospheric absorption lines (courtesy Jose Moreno, University of Valencia). References 1. Plascyk JA, Gabriel FC (1975) Fraunhofer line discriminator MKII: An airborne instrument for precise and standardized ecological luminescence measurement. Ieee T Instrum Meas 24(4):306– 313. 2. Meroni M, et al. (2009) Remote sensing of solar-induced chlorophyll fluorescence: Review of methods and applications. Remote Sens Environ 113(10):2037–2051. 3. Maier SW, Günther KP, Stellmes M (2003) Sun-induced fluorescence: A new tool for precision farming. Digital Imaging and Spectral Techniques: Applications to Precision Agriculture and Crop Physiology, eds van Toai T, Major D, McDonald M, Schepers J, Tartly L (American Society of Agronomy, Inc.; Crop Science Society of American, Inc.; Soil Science Society of American, Inc., Madison, WI), pp 209–222. 4. Sabater N, et al. (2014) A fluorescence retrieval method for the FLEX Sentinel-3 tandem mission. In Workshop on Hyperspectral Imaging and Signal Processing: Evolution in Remote Sensing (WHISPERS) 24 to 27 June 2014, Lausanne, Switzerland. Supplementary information 1 (S2): Ground based measurements for validation Ground-based measurements of sun-induced fluorescence at 760 nm (F760) at the oxygen A-band were collected simultaneously with the airborne overpasses using a high precision portable spectrometer (HR4000, OceanOptics, USA) characterized by a Full Width at Half Maximum (FWHM) of 0.13 nm and a 707 to 805 nm spectral range. The spectrometer was housed in a Peltier thermally regulated box (model NT-16, Magapor, Zaragoza, Spain), keeping the internal temperature at 25 °C in order to reduce dark current drift. The spectrometer was spectrally and radiometrically calibrated with known standards (CAL-2000 mercury argon lamp and LS-1-CAL calibrated tungsten halogen lamp, OceanOptics, USA) before the campaign. The stability of the spectral calibration was regularly assessed during the campaigns using field measured data and the SpecCal algorithm (1, 2). Measurements were acquired every 5 min during flight operations. The nadir-looking, bare-fiber optic was placed 1.4 m top-of-canopy, while the field of view of 25° resulted in a circular area of 0.65 m in diameter. The manual rotation of a horizontally mounted mast allowed the observation of both the vegetated target and the white reference calibrated panel (Labsphere Inc., USA). We acquired spectral data and pre-processed it with a dedicated software package (3). For each data acquisition, spectrometer dark current, incident irradiance, upwelling irradiance, and finally incident irradiance were measured subsequently. We then computed the incident irradiance at the time of target measurement by linear interpolation. The retrieval of F760 was based on the spectral fitting method (SFM) described in Meroni and Colombo (4) and Meroni et al. (1), assuming a linear variation of reflectance and fluorescence in the O2-A absorption band region. The spectral interval used for fluorescence estimation was set to 759.00 to 767.76 nm for a total of 439 spectral channels. According to our knowledge, this is the most accurate method to quantify top-of-canopy fluorescence emission and thus constitutes the best approach for validating airborne fluorescence retrievals. We manually assigned image elements corresponding to the location of ground measurements. We selected pixels covering an area of 20 × 20 m in closest proximity of the ground measurements to account for surface heterogeneity (Fig 2A). Further, a bare-soil field was investigated assuming zero fluorescence emissions during the course of the day. The agreement between retrieved fluorescence signals derived from two contrasting flight heights (i.e., 600 and 1,780 m) was evaluated using an extended set of land cover types (Fig 2B). For each land cover type, a representative area of 200 x 200 m was identified in both images and pixel elements were manually assigned. References 1. Meroni M, et al. (2010) Performance of spectral fitting methods for vegetation fluorescence quantification. Remote Sens Environ 114(2):363–374. 2. Busetto L, Meroni M, Crosta GF, Guanter L, Colombo R (2011) SpecCal: Novel software for infield spectral characterization of high-resolution spectrometers. Comput Geosci-Uk 37(10):1685– 1691. 3. Meroni M, Colombo R (2009) 3S: A novel program for field spectroscopy. Comput Geosci-Uk 35(7):1491–1496. 4. Meroni M, Colombo R (2006) Leaf level detection of detection of solar-induced fluorescence by means of a subnanometer resolution spectroradiometer. Remote Sens Environ 103(4):438–448.