Plants are often subjected to periods of soil and atmospheric water deficits during their life cycle as well as, in many areas of the globe, to high soil salinity. Understanding how plants respond to drought, salt and co-occurring stresses can play a major role in stabilizing crop performance under drought and saline conditions and in the protection of natural vegetation. Photosynthesis, together with cell growth, is among the primary processes to be affected by water or salt stress. The effects of drought and salt stresses on photosynthesis are either direct (as the diffusion limitations through the stomata and the mesophyll and the alterations in photosynthetic metabolism) or secondary, such as the oxidative stress arising from the superimposition of multiple stresses. The carbon balance of a plant during a period of salt/water stress and recovery may depend as much on the velocity and degree of photosynthetic recovery, as it depends on the degree and velocity of photosynthesis decline during water depletion. Current knowledge about physiological limitations to photosynthetic recovery after different intensities of water and salt stress is still scarce. From the large amount of data available on transcript-profiling studies in plants subjected to drought and salt it is becoming apparent that plants perceive and respond to these stresses by quickly altering gene expression in parallel with physiological and biochemical alterations; this occurs even under mild to moderate stress conditions. From a recent comprehensive study that compared salt and drought stress it is apparent that both stresses led to down-regulation of some photosynthetic genes, with most of the changes being small (ratio threshold lower than 1) possibly reflecting the mild stress imposed. When compared with drought, salt stress affected more genes and more intensely, possibly reflecting the combined effects of dehydration and osmotic stress in salt-stressed plants.

There is a long‐standing controversy as to whether drought limits photosynthetic CO₂ assimilation through stomatal closure or by metabolic impairment in C₃ plants. Comparing results from different studies is difficult due to interspecific differences in the response of photosynthesis to leaf water potential and/or relative water content (RWC), the most commonly used parameters to assess the severity of drought. Therefore, we have used stomatal conductance (g) as a basis for comparison of metabolic processes in different studies. The logic is that, as there is a strong link between g and photosynthesis (perhaps co‐regulation between them), so different relationships between RWC or water potential and photosynthetic rate and changes in metabolism in different species and studies may be ‘normalized’ by relating them to g. Re‐analysing data from the literature using light‐saturated g as a parameter indicative of water deficits in plants shows that there is good correspondence between the onset of drought‐induced inhibition of different photosynthetic sub‐processes and g. Contents of ribulose bisphosphate (RuBP) and adenosine triphosphate (ATP) decrease early in drought development, at still relatively high g (higher than 150 mmol H₂O m^–2 s^–1). This suggests that RuBP regeneration and ATP synthesis are impaired. Decreased photochemistry and Rubisco activity typically occur at lower g (<100 mmol H₂O m^–2 s^–1), whereas permanent photoinhibition is only occasional, occurring at very low g (<50 mmol H₂O m^–2 s^–1). Sub‐stomatal CO₂ concentration decreases as g becomes smaller, but increases again at small g. The analysis suggests that stomatal closure is the earliest response to drought and the dominant limitation to photosynthesis at mild to moderate drought. However, in parallel, progressive down‐regulation or inhibition of metabolic processes leads to decreased RuBP content, which becomes the dominant limitation at severe drought, and thereby inhibits photosynthetic CO₂ assimilation.

Drought and salinity are two widespread environmental conditions leading to low water availability for plants. Low water availability is considered the main environmental factor limiting photosynthesis and, consequently, plant growth and yield worldwide. There has been a long‐standing controversy as to whether drought and salt stresses mainly limit photosynthesis through diffusive resistances or by metabolic impairment. Reviewing in vitro and in vivo measurements, it is concluded that salt and drought stress predominantly affect diffusion of CO₂ in the leaves through a decrease of stomatal and mesophyll conductances, but not the biochemical capacity to assimilate CO₂, at mild to rather severe stress levels. The general failure of metabolism observed at more severe stress suggests the occurrence of secondary oxidative stresses, particularly under high‐light conditions. Estimates of photosynthetic limitations based on the photosynthetic response to intercellular CO₂ may lead to artefactual conclusions, even if patchy stomatal closure and the relative increase of cuticular conductance are taken into account, as decreasing mesophyll conductance can cause the CO₂ concentration in chloroplasts of stressed leaves to be considerably lower than the intercellular CO₂ concentration. Measurements based on the photosynthetic response to chloroplast CO₂ often confirm that the photosynthetic capacity is preserved but photosynthesis is limited by diffusive resistances in drought and salt‐stressed leaves.

Chlorophyll a fluorescence (ChlF) has been used for decades to study the organization, functioning, and physiology of photosynthesis at the leaf and subcellular levels. ChlF is now measurable from remote sensing platforms. This provides a new optical means to track photosynthesis and gross primary productivity of terrestrial ecosystems. Importantly, the spatiotemporal and methodological context of the new applications is dramatically different compared with most of the available ChlF literature, which raises a number of important considerations. Although we have a good mechanistic understanding of the processes that control the ChlF signal over the short term, the seasonal link between ChlF and photosynthesis remains obscure. Additionally, while the current understanding of in vivo ChlF is based on pulse amplitude-modulated (PAM) measurements, remote sensing applications are based on the measurement of the passive solar-induced chlorophyll fluorescence (SIF), which entails important differences and new challenges that remain to be solved. In this review we introduce and revisit the physical, physiological, and methodological factors that control the leaf-level ChlF signal in the context of the new remote sensing applications. Specifically, we present the basis of photosynthetic acclimation and its optical signals, we introduce the physical and physiological basis of ChlF from the molecular to the leaf level and beyond, and we introduce and compare PAM and SIF methodology. Finally, we evaluate and identify the challenges that still remain to be answered in order to consolidate our mechanistic understanding of the remotely sensed SIF signal.

During photosynthesis, CO₂ moves from the atmosphere (C_a) surrounding the leaf to the sub‐stomatal internal cavities (C_i) through stomata, and from there to the site of carboxylation inside the chloroplast stroma (C_c) through the leaf mesophyll. The latter CO₂ diffusion component is called mesophyll conductance (g_m), and can be divided in at least three components, that is, conductance through intercellular air spaces (g_ias), through cell wall (g_w) and through the liquid phase inside cells (g_liq). A large body of evidence has accumulated in the past two decades indicating that g_m is sufficiently small as to significantly decrease C_c relative to C_i, therefore limiting photosynthesis. Moreover, g_m is not constant, and it changes among species and in response to environmental factors. In addition, there is now evidence that g_liq and, in some cases, g_w, are the main determinants of g_m. Mesophyll conductance is very dynamic, changing in response to environmental variables as rapid or even faster than stomatal conductance (i.e. within seconds to minutes). A revision of current knowledge on g_m is presented. Firstly, a historical perspective is given, highlighting the founding works and methods, followed by a re‐examination of the range of variation of g_m among plant species and functional groups, and a revision of the responses of g_m to different external (biotic and abiotic) and internal (developmental, structural and metabolic) factors. The possible physiological bases for g_m, including aquaporins and carbonic anhydrases, are discussed. Possible ecological implications for variable g_m are indicated, and the errors induced by neglecting g_m when interpreting photosynthesis and carbon isotope discrimination models are highlighted. Finally, a series of research priorities for the near future are proposed.