On the Estimation Approach of Net Carbon Sequestration Under Non-Continuous Flooding in Rice Fields

Hou et al. (2025) conducted a meta-analysis of field studies from 2019 to 2023 to evaluate the effects of noncontinuous flooding (NCF) practices on net carbon sequestration (NCS) in rice fields. The authors concluded that compared with continuous flooding (CF), NCF substantially enhances ecosystem-scale NCS, primarily by reducing methane (CH₄) emissions while increasing photosynthetic carbon sequestration (PCS), despite a decrease in soil organic carbon (SOC) sequestration. This conclusion, however, warrants further scrutiny regarding methodological assumptions and data representativeness, potentially leading to a systematic overestimation of the carbon sequestration potential of NCF in rice systems.

A primary concern lies in the calculation framework applied to rice systems, where PCS was directly added as a carbon sink component in the NCS budget. PCS represents short-term carbon input via plant photosynthesis, most of which is harvested and rapidly returned to the atmosphere through consumption, combustion, or decomposition. In agricultural systems, only carbon stored long term in soils or stable organic pools is considered true sequestration (Smith et al. 2020). Treating PCS as ecosystem-level carbon sequestration conflates “carbon input” with “carbon retention,” thereby overstating the mitigation potential of carbon sequestration pathways in croplands. This approach also diverges from IPCC guidelines, which emphasize long-term carbon storage as the accounting basis (Ogle et al. 2019). Additionally, since SOC sequestration was estimated by comparing SOC content before and after a single growing season, part of the PCS might have already been reflected in the SOC increment. Adding both PCS and SOC sequestration therefore raises the possibility of double counting in Hou et al. (2025). If the SOC change estimation method proposed by Guan et al. (2023) is adopted, NCS should be calculated based on both the net ecosystem exchange during the rice growing season and non-CO₂ greenhouse gas emissions.

SOC sequestration estimates themselves are also highly uncertain in Hou et al. (2025). Single-season SOC comparisons are vulnerable to sampling error, spatial heterogeneity, and seasonal variability. Numerous studies have shown that detectable SOC changes require multi-year monitoring due to the slow turnover and delayed stabilization of carbon inputs (Smith et al. 2020). Due to the fact that most studies did not incorporate straw return or organic amendments, the reported SOC increase under CF, which exceeds 2800 kg CO₂-eq ha⁻¹ in one season (see figure 7h, Hou et al. 2025), is unusually high. The values of SOC sequestration reported by Hou et al. (2025) substantially exceed estimates from comparable field conditions without external carbon inputs (Lessmann et al. 2022; Liu et al. 2024). Hou et al. also attributed the reduction in SOC sequestration under NCF to increased microbial biomass carbon, implying greater microbial activity and enhanced SOC decomposition. However, increased microbial biomass merely indicates a larger microbial biomass pool and does not necessarily imply higher microbial activity or increased SOC mineralization. Assessing microbial activity requires dynamic, process-based indicators such as respiration rates, enzyme activities, or mineralization fluxes, which were not evaluated in their analysis (Blagodatskaya and Kuzyakov 2013).

Dataset constraints further weaken the conclusions. Only 23 observations from seven publications report complete NCS metrics, including yield, SOC, and non-CO₂ greenhouse gas emissions, with limited geographic coverage and small sample sizes (Figure 1a). Unfortunately, studies published before 2019 were excluded by Hou et al. (2025), despite representing a comparable volume of relevant research (Nikolaisen et al. 2023). Incorporating these earlier data significantly reduces the estimated CH₄ mitigation effect of NCF and may negate or even reverse its yield advantage (Figure 1b). While these factors are beyond the scope of this Letter, it is important to acknowledge that variations in water management practices and the use of organic amendments in rice systems can significantly affect emissions, yield, and SOC dynamics, and should not be overlooked in future assessments.

Jinyang Wang: writing – original draft. Jianwen Zou: writing – review and editing.

The authors declare no conflicts of interest.

This article is a Letter to the Editor regarding Hou et al., https://doi.org/10.1111/gcb.70283. See also the Response to the Letter by Hou et al., https://doi.org/10.1111/gcb.70464.