Critical review: incorporating the arrangement of mitochondria and chloroplasts into models of photosynthesis and carbon isotope discrimination.

The arrangement of mitochondria and chloroplasts, together with the relative resistances of cell wall and chloroplast, determine the path of diffusion out of the leaf for (photo)respired CO2. Traditional photosynthesis models have assumed a tight arrangement of chloroplasts packed together against the cell wall with mitochondria located behind the chloroplasts, deep inside the cytosol. Accordingly, all (photo)respired CO2 must cross the chloroplast before diffusing out of the leaf. Different arrangements have recently been considered, where all or part of the (photo)respired CO2 diffuses through the cytosol without ever entering the chloroplast. Assumptions about the path for the (photo)respiratory flux are particularly relevant for the calculation of mesophyll conductance (gm). If (photo)respired CO2 can diffuse elsewhere besides the chloroplast, apparent gm is no longer a mere physical resistance but a flux-weighted variable sensitive to the ratio of (photo)respiration to net CO2 assimilation. We discuss existing photosynthesis models in conjunction with their treatment of the (photo)respiratory flux and present new equations applicable to the generalized case where (photo)respired CO2 can diffuse both into the chloroplast and through the cytosol. Additionally, we present a new generalized Δ13C model that incorporates this dual diffusion pathway. We assess how assumptions about the fate of (photo)respired CO2 affect the interpretation of photosynthetic data and the challenges it poses for the application of different models.