# A Typical Small Watershed in Southwestern China Is Demonstrated as a Significant Carbon Sink
## 2 Materials and Methods
### Eddy Covariance Data Processing, Gap Filling and Flux Partitioning  
Eddypro 7.0.9 software (LI-COR Biosciences, Lincoln, NE, USA) was used to process the raw 10 Hz flux data. Data processing flow was as follows: data quality control was carried out according to the method recommended by [PERSON] et al. [19], and a double rotation [20] (forest and cropland sites) and planar fit coordinate rotation [21] (non-timber forest site) were used to eliminate the influence of instrument tilt or terrain irregularity on airflow. The effects of air density fluctuations due to heat and water vapor transfer were corrected using Webb-Pearman-Leuning (WPL) correction [22]. Further, flux data were deleted for precipitation time periods. A quality check was performed on the flux data based on internal turbulence tests [23], removing low quality flux data marked as 2. To mitigate the impact of low turbulence on flux data at night time (shortwave incoming global radiation less than 10 W m\({}^{-2}\)), the friction velocity (u*) thresholds (0.26-0.37 m s\({}^{-1}\) for forest dataset, 0.19-0.21 m s\({}^{-1}\) for cropland dataset, and 0.23-0.25 m s\({}^{-1}\) for non-timber forest dataset) determined based on the moving point test (MPT) were applied to filter nighttime carbon flux data [24]. After conducting quality control and u* filtering, the carbon flux datasets for the three sites over two years showed a percentage of missing data ranging from 33.9% to 39.6% (Table 2). The percentage of missing eddy covariance data typically ranged from 20% to 60% and was mainly concentrated at night [25]. Therefore, the rates of missing data at our three sites are reasonable. Missing data was filled using marginal distribution sampling (MDS) [26]. The MDS method has been widely used to fill carbon flux data gaps [18; 25; 27]. It takes into account the temporal autocorrelation of fluxes and the covariance between meteorological variables and fluxes, and uses shortwave incoming global radiation (Rg), air temperature (Tair), and vapor pressure deficit (VPD) to fill the half-hourly NEE. A more detailed description can be found in the paper by [PERSON] et al. [27].The gap filling process was performed using the REddyProC package [27]. \begin{table}
\begin{tabular}{c c c c} \hline \hline \multirow{2}{*}{**Sites**} & **October 2021 to** & **October 2022 to** & \multirow{2}{*}{**Averaged-Gaps (\%)**} \\  & **September 2022 (\%)** & **September 2023 (\%)** & \\ \hline Forest & 41.8 & 25.9 & 33.9 \\ Cropland & 37.2 & 32.7 & 35.0 \\ Non-timber forest & 46.8 & 42.4 & 39.6 \\ \hline \hline \end{tabular}  
* Notes: The count does not include data from non-timber forest site between 1 March and 13 May 2022.  
\end{table} 
Table 2: Percentage of carbon flux data gaps for three eddy covariance sites after quality control and u* filtering. Half-hourly NEE was partitioned into GPP and Re. At night, NEE is equal to Re, when GPP is equal to 0. Based on the half-hourly nighttime data, the relationship between Re and T\({}_{\text{air}}\) was established using Equation (1) [28]:  
\[\text{Re}=\text{R}_{\text{ref}}\cdot exp\bigg{(}\text{E}_{0}\cdot\bigg{(}\frac{1 }{\text{T}_{\text{ref}}-\text{T}_{0}}-\frac{1}{\text{T}_{\text{air}}-\text{T}_ {0}}\bigg{)}\bigg{)} \tag{1}\]  
where Re (umol m\({}^{-2}\) s\({}^{-1}\)) is the ecosystem respiration, R\({}_{\text{ref}}\) (umol m\({}^{-2}\) s\({}^{-1}\)) is the ecosystem respiration rate at a reference temperature (T\({}_{\text{ref}}\)) of 15 \({}^{\circ}\)C, T\({}_{0}\) is kept constant at \(-\)46.02 \({}^{\circ}\)C, E\({}_{0}\) (K) is the activation energy, and T\({}_{\text{air}}\) is air temperature. After Re and T\({}_{\text{air}}\) for the nighttime data were linked through Equation (1), the Re values could be estimated as a function of T\({}_{\text{air}}\) during the daytime. Subsequently, GPP could be calculated using Equation (2):  
\[\text{GPP}=\text{Re}-\text{NEE} \tag{2}\]  
Both Re and GPP were calculated using the REddyProC package [27].