# Progress in Remote Sensing of Photosynthetic Activity over the Amazon Basin
## 1 Introduction  
Tropical forests affect the global climate through their massive exchange of carbon, water and heat. Extensive cloud cover and variable atmospheric conditions, however, make it difficult to estimate these fluxes accurately. In recent decades, precipitation over the Amazon has decreased, along with the length of the wet season [1, 2]. An extension of the dry season decreases photosynthesis while increasing carbon emissions from fires. In the drought of 2005, net ecosystem loss of above-ground growth recorded on intact forest plots was estimated as averaging 5.3 Mg C-ha\({}^{-1}\), with a total loss of between 1.2 and 1.6 Pg for the Amazon Basin [3]. Loss of carbon through ignition can be mappedmoderately accurately, while Gross Primary Production (GPP) is more difficult to assess because the extent that sunlight is absorbed and utilized by photosynthetic tissues is not directly measured with conventional reflectance indices, such as the Normalized Difference Vegetation Index (NDVI) and Enhanced Vegetation Index (EVI). GPP can be modeled as a simple function of the products of incident solar radiation, which is about 50% photosynthetically active (PAR) [4], the faction of that absorbed by photosynthetic tissue (fPAR) and the light-conversion efficiency of photosynthesis (\(\varepsilon\)):  
\[\text{GPP}=\text{PAR}\times\text{f}_{\text{PAR}}\times\varepsilon, \tag{1}\]  
The main challenge in solving Equation (1) is in defining seasonal variation in light use efficiency. Under optimal conditions, absorbed radiation is utilized by the plant to split water (photochemical quenching) and provide electrons for the photosynthetic fixation of CO\({}_{2}\). However, in situations where plants receive more sunlight than they can actually use (i.e., photosynthesis is limited by factors other than light), light use and absorption are adjusted to protect the plant from photo-oxidative damage [5]. When the supply of radiation is in excess, the xanthophyll cycle pigment violaxanthin is converted rapidly via intermediate antheraxanthin to zeaxanthin, and this reaction is reversed when radiation is no longer in excess [5]. This mechanism is called non-photochemical quenching. When heat dissipation increases through non-photochemical quenching, \(\varepsilon\) decreases; consequently leading to a reduction in both chlorophyll fluorescence and fixation of CO\({}_{2}\). The non-photochemical quenching can be quantified by monitoring specific spectral bands to yield a Photochemical Reflectance Index (PRI) [6]:  
\[\text{PRI}=(\rho_{531}-\rho_{570})/(\rho_{531}+\rho_{570}), \tag{2}\]  
where \(\rho_{531}\) is the reflectance at 531 nm, which increases as photosynthesis is downregulated, and \(\rho_{570}\) is the reflectance at 570 nm, which is unresponsive to changes in incident PAR and serves as a reference. A diagram depicting the relevant biophysics is presented in Figure 1, which includes both dissipation of heat and light from chloroplasts. Figure 1: Depiction of the energy pathways within a leaf’s light-harvesting complex. Light is absorbed by antenna pigments and the energy transferred to the reaction center (P680). Under optimal conditions, the energy is used in the dark reaction to fix CO\({}_{2}\) and produce photosynthetic (photochemical quenching). When absorbed light exceeds the capacity of the photosynthetic reactions, the excess energy begins to accumulate in the reaction center, which can lead to photo-oxidative damage to cells. A shift in the type of xanthophyll pigments dissipates this energy as heat at 531 nm or fluorescence from the Fraunhofer lines. Complementary to PRI, Solar-Induced Fluorescence (SIF) may provide further opportunities to measure photosynthetic activity (discussed in Section 3). Although both of these techniques are experimental, they have the potential of providing improved estimates of GPP at increasingly refined temporal and spatial resolutions, as seen in [7; 8; 9].