Metabolomics of related C3 and C4 Flaveria species indicate differences in the operation of photorespiration under fluctuating light

C₃ photosynthesis can be complemented with a C₄ carbon concentrating mechanism (CCM) to minimize photorespiratory losses. C₄ photosynthesis is often more efficient than C₃ under steady-state conditions. However, the C₄ CCM depends on inter-cellular metabolite concentration gradients, which must increase following increases in light intensity and could decrease rates of C₄ photosynthesis under fluctuating light. Additionally, incomplete flux through photorespiration could prove beneficial to C₄ assimilation during light induction of the CCM. Here, we compare metabolic profiles in the closely related C₃ <i>Flaveria robusta</i> and C₄ <i>Flaveria bidentis</i> during a light transient from low to high light to determine if these non-steady state accumulation patterns provide insight to the induction of the metabolite gradients needed to drive C4 intermediate transport and if there is incomplete cycling of photorespiratory intermediates. In these C₃ and C₄ species, metabolite steady-state pool sizes suggest that C₄ transport acids maintain concentration gradients across the bundle sheath and mesophyll cell types under these light fluctuations. However, there was incomplete flux through photorespiration in the C₄ <i>F. bidentis</i>, which could reduce photorespiratory CO₂ loss via glycine decarboxylation and help maintain higher rates of assimilation during following induction periods.