## 2 Materials and Methods
### Soil Collection and Gas Sampling
#### 2.1.2 Measurement of Soil Respiration  
Static dark boxes with 50 cm \(\times\) 50 cm \(\times\) 50 cm were used as a field gas collection device, with the boxes raised as plant heights changed. The box was constructed polyethylene (PVC) covered with foam and reflective material and had a fan for mixing gases inside the box installed on the top along with a gas collection port. The gas was collected in a vacuum bag using a syringe from 9:00 to 9:30 on the above-mentioned soil sample collection date. Each sample collection point needs to be separated by 10 min for continuous gas collection. Temperature was measured with a thermometer (JM624, Guangzhou, China) at 5 cm depth. Three rice plants were randomly collected from each sample site during rice harvesting and then dried in oven at 105 \({}^{\circ}\)C until achieving. Gas samples were immediately brought to the laboratory for quantification of CO\({}_{2}\) using an Agilent 7890 B gas chromatograph-massspectrometer (Agilent, Santa Clara, CA, USA) with a hydrogen flame ion detector (FID). An external standard working curve was plotted after running every 48 samples. The gas emission rate (_dc/dt_) was derived from the slope of four consecutive sample concentration values using linear regression analysis. Greenhouse gas emission flux was calculated using the following equation:  
\[F=H\frac{MP}{R(273+T)}\frac{dc}{dt} \tag{1}\]  
where \(F\) is the gas emission flux (units of mg\(\cdot\)m\({}^{-2}\).h\({}^{-1}\)); \(H\) is the height of the sampling box (m); \(M\) is the molar mass of gas (g\(\cdot\)mol\({}^{-1}\)); \(P\) is the air pressure at the sampling point (Pa); \(R\) is the universal gas constant (8.314, Pa\(\cdot\)m\({}^{-3}\cdot\)mol\({}^{-1}\cdot\)k\({}^{-1}\)); T is the average temperature inside the box at the time of sampling (\({}^{\circ}\)C) and dc/dt is the gas emission rate (uL\(\cdot\)L\({}^{-1}\cdot\)min\({}^{-1}\)). Heterotrophic respiration (\(R_{h}\)) was then calculated using the following equations:  
\[NPP=NPP_{\text{seeds}}+NPP_{\text{straw}}+NPP_{\text{roots}}+NPP_{\text{ apoplast}}+NPP_{\text{root\,sediment}} \tag{2}\]  
\[GPP=NPP+R_{\text{a}} \tag{3}\]  
\[R_{\text{h}}=R_{\text{e}}-R_{\text{a}} \tag{4}\]  
where \(NPP\) is the total carbon added to the above- and below-ground portions of the plant during the entire growth cycle (kg\(\cdot\)hm\({}^{-2}\)); \(NPP_{\text{seeds}}\) and \(NPP_{\text{straw}}\) are the estimated biomass from the harvested plants after drying, while \(NPP_{\text{root}}\), \(NPP_{\text{apoplast}}\) and \(NPP_{\text{root\,sediment}}\) were estimated by referencing previous studies [30; 31; 32]. The equation assumed an above-ground/root system ratio for rice of 1.0/0.1, and apoplankton coverage of 5% and 8% of the upper and root dry biomass, respectively, and root sediment accounted for 15% of the total plant biomass. In Equation (3), \(GPP\) is total primary productivity, \(R_{\text{a}}\) is autotrophic respiration (unit: kg\(\cdot\)hm\({}^{-2}\)), and the \(NPP/GPP\) ratio is 0.58 [34]. In Equation (4), \(R_{\text{e}}\) is ecosystem respiration and \(R_{\text{h}}\) is heterotrophic respiration (kg\(\cdot\)hm\({}^{-2}\)). The cumulative greenhouse gas (single-season rice) emissions were calculated as follows:  
\[E\text{c}=\left[\frac{F_{\text{I}}+F_{n}}{2}+\sum_{i=1}^{n}\left(\frac{F_{i}+ F_{i+1}}{2}\right)\times\left(t_{i+1}-t_{i}\right)\right]\times 24\times 0.01\times a \tag{5}\]  
where \(E_{\text{c}}\) is cumulative greenhouse gas (single-season rice) emissions (kg\(\cdot\)hm\({}^{-2}\)); \(n\) is the number of observations during a single rice season; \(i\) is the sampling interval, \(F_{i}\) and \(F_{i+1}\) are the GHG emission fluxes (mg\(\cdot\)m\({}^{-2}\cdot\)h\({}^{-1}\)) at the \(i\)th and \(i+1\)th sampling, respectively; \(F_{1}\) and \(F_{n}\) are the GHG emission fluxes at the first and last sampling times, respectively; \(t_{i+1}\) and \(t_{\text{i}}\) are the time intervals (d) between the \(i+1\)th and \(i\)th sampling; and a is a conversion factor of 98/94.