Comparison of the eddy covariance and automated closed chamber methods for evaluating nocturnal CO2 exchange in a Japanese cypress forest

Underestimation of nocturnal CO2 respiration using the eddy covariance method under calm conditions remains an unsolved problem at many flux observation sites in forests. To evaluate nocturnal CO2 exchange in a Japanese cypress forest, we observed CO2 flux above the canopy (Fc), changes in CO2 storage in the canopy (St) and soil, and trunk and foliar respiration for 2 years (2003–2004). We scaled these chamber data to the soil, trunk, and foliar respiration per unit of ground area (Fs, Ft, Ff, respectively) and used the relationships of Fs, Ft, and Ff with air or soil temperature for comparison with canopy-scale CO2 exchange measurements (=Fc + St). The annual average Fs, Ft, and Ff were 714 g C m−2 year−1, 170 g C m−2 year−1, and 575 g C m−2 year−1, respectively. At small friction velocity (u*), nocturnal Fc + St was smaller than Fs + Ft + Ff estimated using the chamber method, whereas the two values were almost the same at large u*. We replaced Fc + St measured during calm nocturnal periods with a value simulated using a temperature response function derived during well-mixed nocturnal periods. With this correction, the estimated net ecosystem exchange (NEE) from Fc + St data ranged from −713 g C m−2 year−1 to −412 g C m−2 year−1 in 2003 and from −883 g C m−2 year−1 to −603 g C m−2 year−1 in 2004, depending on the u* threshold. When we replaced all nocturnal Fc + St data with Fs + Ft + Ff estimated using the chamber method, NEE was −506 g C m−2 year−1 and −682 g C m−2 year−1 for 2003 and 2004, respectively.