Dynamic photosynthesis under a fluctuating environment: a modelling-based analysis

In their natural environment, leaves are exposed to rapid fluctuations of irradiance. Research on CO2 assimilation under fluctuating irradiance often relies on measurements of gas exchange during transients where irradiance is rapidly increased or decreased, after the leaf has adapted to a particular set of environmental conditions. In the field, such increases and decreases occur mostly because of sunflecks (rapid increases in irradiance on a low irradiance background) created by gaps in the canopy and plant movement by wind, and cloudflecks (rapid decreases in irradiance on a high irradiance background) generated by clouds that transiently block the sun. In this dissertation, the metabolic regulation of photosynthesis and how this may limit dynamic CO2 assimilation is studied <em>in silico</em> with the development and application of simulation models. In order to support the development of the models, a review of the literature was performed as well as an experiment designed to generate data on dynamic CO2 assimilation for different photosynthetic mutants of <em>Arabidopsis thaliana</em>. In addition to providing these models to the research community, this dissertation also identifies multiple targets that may be used for improving dynamic CO2 assimilation in plants. It further demonstrates that the dynamic responses of CO2 assimilation to changes in irradiance has a significant effect on canopy CO2 assimilation, even for dense canopies exposed to open skies, resembling the conditions of commercial crops. In <strong>Chapter 1</strong>, the context of this dissertation is presented. The societal relevance of this research is argued, making reference to the role that photosynthesis could play in addressing global problems such as food and energy security. The necessary background on the physiology of photosynthesis is provided, with special emphasis on the terminology and concepts required to understand the rest of the dissertation, with the aim of making the contents more accessible to a wider audience. Then, prior literature on the specific topics of this dissertation (i.e., photosynthesis in a dynamic environment and its mathematical modelling) is presented, with a chronological approach that analyses the evolution of ideas and methodologies up to the present. In <strong>Chapter 2</strong>, the current literature on dynamic CO2 assimilation is reviewed, with an emphasis on the effects of environmental conditions ([CO2], temperature, and air humidity) on the rates of photosynthetic induction and loss of induction. This review reveals major knowledge gaps, especially on the loss of induction. The little data available indicates that rates of photosynthetic induction increase with [CO2], which could be explained by a weak effect on Rubisco activation and a strong effect on stomatal opening. Increases in temperature also increase the rates of photosynthetic induction, up to an optimum, beyond which a strong negative effect can be observed, which could be attributed to deactivation of Rubisco activase. In <strong>Chapter 3</strong>, an experiment is presented that makes use of several photosynthetic mutants of <em>A. thaliana</em>. Downregulating non-photochemical quenching and sucrose synthesis did not have any significant effect on dynamic CO2 assimilation, whereas CO2 diffusion and Rubisco activation exerted stronger limitations. Further analysis reveals that whether stomatal opening limits CO2 assimilation after an increase in irradiance depends on the stomatal conductance prior to the change in irradiance. A threshold value of 0.12 mol m−2 s−1 (defined for fluxes of water vapour) could be defined, above which stomata did not affect the rates of photosynthetic induction. The comparison of measurements across irradiance levels also indicated that the apparent rate constant of Rubisco activation is irradiance-dependent, at least for irradiance levels below 150 μmol m−2 s−1. In <strong>Chapter 4</strong>, a phenomenological model of leaf-level CO2 assimilation is presented. The model is described in detail and all the parameters are first estimated with published data, and later refined by fitting the model to the data from Chapter 3. Additional data from the experiment in Chapter 3 is used to validate predictions of CO2 assimilation under lightflecks for the different photosynthetic mutants. The model predicts accurately dynamic CO2 assimilation for the different photosynthetic mutants by only modifying those parameters that are affected by the mutation. This demonstrates that the model has a high predictive power and that the equations, although phenomenological in nature, have a solid physiological basis. The model is further used to analyse, <em>in silico</em>, the limitations imposed by different photosynthetic processes on dynamic CO2 assimilation at the leaf and canopy level, allowing a more in depth analysis than in Chapter 3. The analysis demonstrates that results obtained at the leaf level should not be extrapolated directly to the canopy level, as the spatial and temporal distribution of irradiance within a canopy is more complex than what is achieved in experimental protocols. Both at the leaf and canopy level, CO2 diffusion is strongly limiting, followed by photoinhibition, chloroplast movements and Rubisco activation. In <strong>Chapter 5</strong>, a mechanistic model of the dynamic, metabolic regulation of the electron transport chain is presented. The model is described in detail and all the parameters are estimated from published literature, using measurements on <em>A. thaliana</em> when available. Predictions of the model are tested with steady-state and dynamic measurements of gas exchange, chlorophyll fluorescence and absorbance spectroscopy on <em>A. thaliana</em>, with success. The analysis <em>in silico</em> indicates that a significant amount of alternative electron transport is required to couple ATP and NADPH production and demand, and most of it is associated with nitrogen assimilation and export of redox power through the malate shuttle. The analysis also reveals that the relationship between ATP synthesis and the proton motive force is highly regulated by the concentrations of substrates (ADP, ATP and inorganic phosphate), and this regulation facilitates an increase in non-photochemical quenching under conditions of low metabolic activity in the stroma. In <strong>Chapter 6</strong>, the findings of Chapters 2–5 are summarised and employed to answer in detail the four research questions formulated in Chapter 1. Of great interest is the identification of six potential targets that may be used to improve dynamic CO2 assimilation. These targets are: (i) regulation of Rubisco activity through changes in the amount or regulation of Rubisco activase, (ii) acceleration of stomatal opening and closure, (iii) a lower /ATP for ATP synthesis, (iv) faster relaxation of non-photochemical quenching, (v) reduced chloroplast movements, and (vi) reduced photoinhibition by increased rates of repair of Photosystem II.