# Adjustments to SIF Aid the Interpretation of Drought Responses at the Caatinga of Northeast Brazil
## 4 Discussion
### SIF Seasonality and Phenological Processes  
In much of the Caatinga, SIF yearly minimum values were often about a quarter of the yearly maximum values (results not shown), characterizing a large seasonal variation in SIF (Figure 4). For most plants, physiological responses to heat and drought stress generally consist in adaptive measures like: limiting water loss through the closing of stomata and the consequent lowering of the photochemical quenching (qP) and fluorescence emissions [44]; Moreover, dissipating excess-energy through the Non-Photochemical Quenching (NPQ) pathways, which lowers fluorescence emissions, since these processes \"compete\" for the same energy [4; 7; 8]. Therefore, the more energy is dissipated through NPQ the less will be left for qP and its associated fluorescence emission. Nonetheless, since we are observing seasonal phenomena, not all variation can be attributed to physiology.  
A study testing the effects of the exposure of plants to the combined stresses of drought and high-temperature at the leaf-level reported a five-fold decrease in fluorescence emissions that couldn't be attributed only to photoadaptive processes such as qP and NPQ but, was instead found to be largely the result of chlorophyll degradation [88]. Similarly, the marked decrease in SIF emissions observed concomitantly with the ecoregion-specific dry seasons (Figure 4) suggests a combined effect of seasonal photosynthesis adaptation (e.g., non-transient lowering of qP and the increasing of NPQ) and phenological processes like chlorophyll degradation and leaf-shedding. These phenological processes are known to play a major role in the Caatinga's vegetation dynamics [39] and it is reasonable to expect that they must account for much of the observed SIF seasonal variation. This is further supported by the sampled SVI seasonality which adheres closely to SIF seasonality (results not shown) and correlates well to SIF data at most ecoregions (Figure 10 and Appendix A Table A4). Nevertheless, even at the tested monthly scale, these processes are not the exclusive source of SIF output variation as is proven by SIF\({}_{FR}\)-Yield LMM results (Table 2). While the influences of phenological processes (e.g., leaf flushing, leaf maturation, chlorophyll degradation and leaf shedding) must be considered carefully, our results show that they do not invalidate the interpretation of chlorophyll fluorescence seasonality and stress responses.  
Furthermore, the reversal in SIF\({}_{FR}\) and SIF\({}_{R}\) emission levels observed at the onset of the dry season (Figure 4) is consistent with the expected effects of leaf shedding and chlorophyll degradation on the reabsorption of SIF\({}_{R}\)[14; 15] but, this effect is shown here with fluorescence emitted by a large sample of plants instead of that emitted by a single leaf as described by [PERSON] [13]. To our knowledge, this is the only study showing the relationship between the SIF\({}_{R/FR}\) ratio and chlorophyll content at the community level in the seasonal scale, as it is demonstrated by the seasonality of SIF\({}_{FR}\) and SIF\({}_{R}\) emission levels (Figure 4), and also demonstrated at an anomalous drought by our trend analysis (Figure 5, year 2012). However, LMM results show that SIF\({}_{R/FR}\) variation is mostly driven by the phenological cycle as the effect of seasonality was constrained in our models though random factors and SIF\({}_{R/FR}\) was not significantly affected by any fixed factor (Table 2).