What gas exchange data can tell us about photosynthesis
This title is a modification of the title of Long and Bernacchi (2003), who described the then current state of analysis of A/Ci curves, plots of photosynthetic CO2 assimilation versus CO2 inside the leaf (to remove any influence of stomata). These curves were made possible by the concept of a calculated CO2 partial pressure inside a leaf (Moss & Rawlins 1963) and have been studied since the 1970s when Graham Farquhar was a post-doc and I was a graduate student in Klaus Raschke's lab. In 1980, Farquhar, von Caemmerer and Berry (1980) published a seminal paper describing photosynthesis as either ‘Rubisco limited’ or ‘RuBP limited’, and soon, a third limitation was added, ‘TPU limited’ (Sharkey 1985). A/Ci curves are ideally suited to assess these three mechanisms that can set the upper limit to the rate of photosynthesis. Analyses of A/Ci curves and the tripartite model of photosynthesis limitations have been very useful for testing mechanistic models of photosynthetic metabolism and for predicting photosynthetic responses to global change (Wullschleger 1993). This issue of Plant, Cell & Environment, includes several papers related to the analysis of gas exchange data (Bellasio et al. 2015b; Bellasio et al. 2015a; Walker & Ort 2015). Here, I highlight the importance of these contributions and also announce an update to the PCE Calculator (version 2.0) that can be used for a simple analysis of gas exchange parameters from A/Ci curves. A separate sheet is provided to fit light response curves following the recommendations of Buckley and Diaz-Espejo (2015). The success of the Farquhar, von Caemmerer and Berry (1980) model derives at least in part because it allows gas exchange measurements to be interpreted in terms of biochemical and biophysical processes. Soon after publication of the model, programs and algorithms for estimating the underlying parameters became available. One early program was provided by Dundee Scientific (Dundee, Scotland) and called ‘Photosyn Assistant’ (http://www.ddsci.com/). Several other methods were shared informally among researchers, including one by Carl Bernacchi that used linear versions of some of the equations so that critical parameters could be estimated from linear regressions. In 2007, PC&E made available an Excel spreadsheet to help estimate key parameters from A/Ci curves (Sharkey et al. 2007). The intent was to strike a balance between detailed information and ease of use. Theoretically, five parameters could be estimated: Vcmax, J, TPU, Rd and gm (the maximum carboxylation rate of Rubisco, maximum rate of electron transport for the given light intensity, maximum rate of triose phosphate use, day respiration, and mesophyll conductance to CO2 transfer, respectively). With five parameters that can be adjusted, some very good fits are possible, even if they are not always believable. Instead, each parameter should be considered carefully, and when possible, parameters should be fixed using other data to improve estimates of the remaining parameters. Since the publication of this tool in 2007, a number of issues have become more clear about each of the parameters, as outlined in the following. This technique has been used by many people, but what is not clear in the publications is that the lines often do not intersect that well, creating uncertainty in the intersection point. In this issue of PC&E, Walker and Ort (2015) provide a method for analysing Γ* data so that the effects of small errors and uncertainties are minimized, giving a more robust estimate of Γ*. A new estimate of Γ* over a range of temperature has been determined for Arabidopsis thaliana (Weise et al. 2015), and a new spreadsheet in the PCE Calculator with an Arabidopsis thaliana Γ* value is now available (version 2.0 (A)). When reverse sensitivity is observed at high CO2 in an A/Ci curve, a second new sheet (2.0 (R)) is provided that estimates α, an arbitrary parameter useful for describing the degree of decline of photosynthesis with increasing CO2 at high CO2. As before, the PCE Calculator requires the user to assign which points are controlled by Rubisco, which by RuBP regeneration and which by TPU. The most informative data points are the RuBP-regeneration-limited data points, and so, investigators should be sure to include many points in this region. The fitting program of Gu et al. (2010) estimates these transitions within the program and allows users to share data at the website leafweb.ornl.gov. Now an even more detailed approach is available in the supplemental material of Bellasio et al. (2015b), who provide a series of worksheets that allows estimation of many more parameters. This is a comprehensive analysis of photosynthesis making use of A/Ci curves at normal and low oxygen and light response curves. Carrying out such a comprehensive analysis will likely be challenging, but also very rewarding because of the rich dataset that will be obtained. Finally, Bellasio et al. (2015a) extend this type of A/Ci curve analysis to C4 plants. Because the C4 pump obscures many of the C3 processes, the C4 analysis is less mechanistic, but very interesting data can still come from this analysis. It was not obvious in 1980 that the mechanistic model of photosynthesis would have such far-reaching implications. The original paper has been cited over 4900 times according to Google Scholar, and the peak in the number of citations came in 2013, 33 years after its publication. One reason for its popularity is that underlying biochemical mechanisms can be estimated from leaf gas exchange characteristics. The papers in this issue (Bellasio et al. 2015b; Bellasio et al. 2015a; Walker & Ort 2015) and the updated version of the PCE Calculator should continue the usefulness of analysis of A/Ci curves and allow ever greater information to be obtained by gas analysis of photosynthesis. My work on photosynthesis is funded by the US Department of Energy grant DE-SCOOO8509 and by USDA for support of my salary. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.