Abstract. CO2 storage (Fs) is the cumulation or depletion in CO2 amount over a period in an ecosystem. Along with the eddy covariance flux and wind-stream advection of CO2, it is a major term in the net ecosystem CO2 exchange (NEE) equation. The CO2 storage dominates the NEE equation under a stable atmospheric stratification when the equation is used for forest ecosystems over complex terrains. However, estimating Fs remains challenging due to the frequent gusts and random fluctuations in boundary-layer flows that lead to tremendous difficulties in capturing the true trend of CO2 changes for use in storage estimation from eddy covariance along with atmospheric profile techniques. Using measurements from Qingyuan Ker Towers equipped with NEE instrument systems separately covering mixed broad-leaved, oak, and larch forest towers in a mountain watershed, this study investigates gust periods and CO2 fluctuation magnitudes and examines their impact on Fs estimation in relation to the terrain complexity index (TCI). The gusts induce CO2 fluctuations for numerous periods of 1 to 10 min over 2 h. Diurnal, seasonal, and spatial differences (P < 0.01) in the maximum amplitude of CO2 fluctuations (Am) range from 1.6 to 136.7 ppm, and these differences range from 140 to 170 s in a period (Pm) at the same significance level. Am and Pm are significantly correlated to the magnitude of and random error in Fs with diurnal and seasonal differences. These correlations decrease as CO2 averaging time windows become longer. To minimize the uncertainties in Fs, a constant [CO2] averaging time window for the Fs estimates is not ideal. Dynamic averaging time windows and a decision-level fusion model can reduce the potential underestimation of Fs by 29 %–33 % for temperate forests in complex terrain. In our study, the relative contribution of Fs to the 30 min NEE observations ranged from 17 % to 82 % depending on turbulent mixing and the TCI. The study's approach is notable as it incorporates the TCI and utilizes three flux towers for replication, making the findings relevant to similar regions with a single tower.
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