Chlorophyll (Chl) a fluorescence induction (transient), measured by exposing dark-adapted samples to high light, shows a polyphasic rise, which has been the subject of extensive research over several decades. Several Chl fluorescence parameters based on this transient have been defined, the most widely used being the F_V [= (F_M–F₀)]/F_M ratio as a proxy for the maximum quantum yield of PSII photochemistry. However, considerable additional information may be derived from analysis of the shape of the fluorescence transient. In fact, several performance indices (PIs) have been defined, which are suggested to provide information on the structure and function of PSII, as well as on the efficiencies of specific electron transport reactions in the thylakoid membrane. Further, these PIs have been proposed to quantify plant tolerance to stress, such as by high light, drought, high (or low) temperature, or N-deficiency. This is an interesting idea, since the speed of the Chl a fluorescence transient measurement (<1 s) is very suitable for high-throughput phenotyping. In this review, we describe how PIs have been used in the assessment of photosynthetic tolerance to various abiotic stress factors. We synthesize these findings and draw conclusions on the suitability of several PIs in assessing stress responses. Finally, we highlight an alternative method to extract information from fluorescence transients, the Integrated BiomarkerResponse. This method has been developed to define multi-parametric indices in other scientific fields (e.g., ecology), and may be used to combine Chl a fluorescence data with other proxies characterizing CO₂ assimilation, or even growth or grain yield, allowing a more holistic assessment of plant performance.

With limited agricultural land and increasing human population, it is essential to enhance overall photosynthesis and thus productivity. Oxygenic photosynthesis begins with light absorption, followed by excitation energy transfer to the reaction centres, primary photochemistry, electron and proton transport, NADPH and ATP synthesis, and then CO₂ fixation (Calvin–Benson cycle, as well as Hatch–Slack cycle). Here we cover some of the discoveries related to this process, such as the existence of two light reactions and two photosystems connected by an electron transport ‘chain’ (the Z-scheme), chemiosmotic hypothesis for ATP synthesis, water oxidation clock for oxygen evolution, steps for carbon fixation, and finally the diverse mechanisms of regulatory processes, such as ‘state transitions’ and ‘non-photochemical quenching’ of the excited state of chlorophyll a. In this review, we emphasize that mathematical modelling is a highly valuable tool in understanding and making predictions regarding photosynthesis. Different mathematical models have been used to examine current theories on diverse photosynthetic processes; these have been validated through simulation(s) of available experimental data, such as chlorophyll a fluorescence induction, measured with fluorometers using continuous (or modulated) exciting light, and absorbance changes at 820 nm (ΔA₈₂₀) related to redox changes in P700, the reaction centre of photosystem I. We highlight here the important role of modelling in deciphering and untangling complex photosynthesis processes taking place simultaneously, as well as in predicting possible ways to obtain higher biomass and productivity in plants, algae and cyanobacteria.

Chlorophyll a fluorescence rise caused by illumination of photosynthetic samples by high intensity of exciting light, the O–J–I–P (O–I1–I2–P) transient, is reviewed here. First, basic information about chlorophyll a fluorescence is given, followed by a description of instrumental set-ups, nomenclature of the transient, and samples used for the measurements. The review mainly focuses on the explanation of particular steps of the transient based on experimental and theoretical results, published since a last review on chlorophyll a fluorescence induction [Lazár D (1999) Biochimica et Biophysica Acta1412, 1–28]. In addition to ‘old’ concepts (e.g. changes in redox states of electron acceptors of photosystem II (PSII), effect of the donor side of PSII, fluorescence quenching by oxidised plastoquinone pool), ‘new’ approaches (e.g. electric voltage across thylakoid membranes, electron transport through the inactive branch in PSII, recombinations between PSII electron acceptors and donors, electron transport reactions after PSII, light gradient within the sample) are reviewed. The K-step, usually detected after a high-temperature stress, and other steps appearing in the transient (the H and G steps) are also discussed. Finally, some applications of the transient are also mentioned.

Current methods of in-house plant phenotyping are providing a powerful new tool for plant biology studies. The self-constructed and commercial platforms established in the last few years, employ non-destructive methods and measurements on a large and high-throughput scale. The platforms offer to certain extent, automated measurements, using either simple single sensor analysis, or advanced integrative simultaneous analysis by multiple sensors. However, due to the complexity of the approaches used, it is not always clear what such forms of plant phenotyping can offer the potential end-user, i.e. plant biologist. This review focuses on imaging methods used in the phenotyping of plant shoots including a brief survey of the sensors used. To open up this topic to a broader audience, we provide here a simple introduction to the principles of automated non-destructive analysis, namely RGB, chlorophyll fluorescence, thermal and hyperspectral imaging. We further on present an overview on how and to which extent, the automated integrative in-house phenotyping platforms have been used recently to study the responses of plants to various changing environments.