Separation of the photosynthetic (F-P) and respiratory (F-R) fluxes of net CO2 exchange (F-N) remains a necessary step toward understanding the biological and physical controls on carbon cycling between the soil, biomass, and atmosphere. Despite recent advancements in stable carbon isotope partitioning methodology, several potential limitations can cause uncertainty in the partitioned results. Here, we combined an automated chamber system with a tunable diode laser (TDL) to evaluate carbon isotope partitioning under controlled environmental conditions. Experiments were conducted in a climate controlled greenhouse utilizing both soybean (C-3 pathway) and corn (C-4 pathway) treatments. Under these conditions, net exchange of (CO2)-C-13 and (CO2)-C-12 was obtained with an improved signal to noise ratio. Further, the chamber system was used to estimate soil evaporation (E) and plant transpiration (T), allowing for an improved estimate of the total conductance to CO2 (g(c)). This study found that the incorporation of short-term and diel variability in the isotope composition of respiration (delta(R)) caused F-P to nearly double in the corn system while only slightly increasing in the soybean system. Variability in both g(c) and the CO2 bundle sheath leakage factor for C-4 plants (phi) also had a significant influence on F-P. In addition, chamber measurements of F-N and its isotope composition (delta(N)) indicated that post-illumination processes caused a decrease in plant respiration for up to 3 h following light termination. Finally, this study found systematic differences between the isotope and temperature-regression partitioning methods on the diel time scale. Published by Elsevier B.V.
