Unlocking the carbon secrets of flooded rice fields
New research reveals how iron and microbes drive greenhouse gas emissions and carbon fate in paddy soils
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Mechanism and modeling of biogeochemical turnover of organic carbon fractions in paddy soil during flooding process
view moreCredit: Chengli Hu, Pei Wang & Tongxu Liu
Paddy soils are critical ecosystems for global food security, yet also significant contributors to atmospheric greenhouse gases like methane and carbon dioxide. These unique wetland environments, characterized by prolonged flooding, play a complex role in the global carbon cycle. Scientists at the Guangdong Academy of Sciences and South China Normal University undertook a detailed investigation to understand the specific biogeochemical turnover of organic carbon fractions within these soils during flooding. This work aims to unravel the intricate mechanisms that govern carbon's fate, helping to predict and manage emissions from these vast agricultural lands.
Iron's Dual Role in Carbon Turnover
The research team, led by Tongxu Liu, utilized a 40-day anoxic microcosm cultivation experiment to simulate flooding conditions. They discovered that iron minerals, initially protecting organic carbon, undergo a significant transformation under oxygen-depleted conditions. This reductive dissolution of iron minerals destabilizes soil aggregates, releasing previously bound organic carbon. This initial "release process" during the first 20 days accounts for a substantial decrease in the inert carbon pool, making carbon more accessible for microbial activity.
Microbial Shifts Drive Greenhouse Gas Production
As flooding progresses, microbial communities adapt and take over as the primary drivers of carbon turnover. The study identified a shift towards dominant genera such as Clostridium and Fonticella in the later stages. These microbes are crucial in driving both iron cycling and methane production. This microbial decomposition phase, particularly after 20 days, leads to a marked increase in potent greenhouse gas emissions, with methane becoming increasingly dominant over carbon dioxide.
Quantifying Carbon Pathways with a Kinetic Model
To quantify these dynamic processes, the researchers developed a sophisticated kinetic model. This model elucidated the intricate pathways and rates of carbon transformation between active, chronic, and inert organic carbon pools. It revealed that while the inert carbon pool rapidly converts into active fractions, these active pools are then quickly decomposed and mineralized into CH₄ and CO₂. The model also explains the accumulation of the chronic carbon pool, attributing it to its inherent molecular persistence and resistance to further breakdown, despite significant transformation from the inert pool.
The study provides compelling quantitative insights into these transformations. During the 40-day flooding period, the active carbon pool saw a modest decrease, while the inert carbon pool dropped by nearly 14% of the total soil organic carbon. Concurrently, the chronic carbon pool increased by a comparable 14.36%. This dynamic interplay results in a net decrease in overall carbon stability within paddy soils, directly impacting the amount of greenhouse gases released into the atmosphere.
Informing Sustainable Carbon Management
These findings have profound implications for agricultural practices and climate change mitigation. Understanding the specific mechanisms and rates of carbon turnover, particularly the role of iron reduction and microbial shifts, allows for more accurate predictions of greenhouse gas emissions from paddy fields. The model provides a theoretical framework for developing strategies to enhance carbon sequestration and reduce emissions in these critical agricultural ecosystems. Future investigations will delve into the influence of varying soil iron contents and additional dynamic experiments to refine the model's predictive power.
Suggested author quote for approval:
"Our research reveals that the long-term flooding of paddy soils triggers a complex dance between minerals and microbes, dictating whether carbon is stored or released as powerful greenhouse gases," says Tongxu Liu, a corresponding author from the Guangdong Academy of Sciences. "Quantifying these processes through our kinetic model is a vital step toward better carbon management and emission reduction in these essential agricultural landscapes."
Corresponding Author: Tongxu Liu
Original Source: https://doi.org/10.1007/s44246-026-00273-5
Contributions: All authors contributed to the study conception and design. Investigation and data analysis were performed by Chengli Hu, Pei Wang, Yang Yang, Kuan Cheng, Wenting Chi, Chao Guo, Guojun Chen and Zebin Hong. Supervision was provided by Tongxu Liu and Xiaomin Li. The first draft of the manuscript was written by Chengli Hu and Pei Wang, and Shiwen Hu, Xiaomin Li and Tongxu Liu commented on previous versions of the manuscript. All authors read and approved the final manuscript.
Journal
Carbon Research
Method of Research
Experimental study
Subject of Research
Not applicable
Article Title
Mechanism and modeling of biogeochemical turnover of organic carbon fractions in paddy soil during flooding process
Article Publication Date
16-Jun-2026
COI Statement
Tongxu Liu is an editorial board member of Carbon Research and was not involved in the editorial review, or the decision to publish, this article. All authors declare that there are no competing interests.
Researchers uncover "intelligent molecular module" for rice chilling recovery and nitrogen use efficiency
Global climate change has increased the frequency of regional cold spells, causing substantial yield losses and even crop failure. Meanwhile, excessive nitrogen fertilizer use in agriculture has increased non-point-source pollution. Improving both stress resilience and nitrogen use efficiency has therefore become a major challenge for sustainable crop production.
In rice production, farmers commonly apply nitrogen fertilizer after chilling stress to stimulate tiller regeneration and reduce yield loss. Although this practice is widely used, it increases production costs and environmental impacts. Furthermore, the molecular mechanism linking post-chilling recovery with nitrogen utilization had not been well understood.
Now, a team led by Prof. CHONG Kang from the Institute of Botany of the Chinese Academy of Sciences has identified what it calls an "intelligent molecular module," Chilling Phoenix (CHPO), which coordinates chilling resilience and nitrogen use in rice by automatically changing its function depending on environmental conditions. During chilling stress, CHPO enhances chilling tolerance. Conversely, when temperatures return to normal, CHPO promotes nitrogen uptake and tiller regeneration during recovery.
The study was published in Nature on June 17.
To provide a framework for their study, the researchers established the post-chilling tiller regeneration rate as a key indicator of chilling resilience. They subsequently employed genome-wide association studies (GWAS), quantitative trait locus (QTL) mapping, and map-based cloning to identify CHPO as a key genetic module that jointly regulates chilling resilience and nitrogen use efficiency.
The researchers identified two alleles: The superior allele, CHPOjap, originated from Chinese common wild rice and was positively selected during the domestication of temperate japonica rice. Compared with CHPOjap, the indica allele CHPOind carries a different number of GCG repeats in its coding region, leading to distinct cold responses, DNA-binding preferences, and contrasting effects on chilling resilience.
Mechanistic analyses revealed that CHPOjap dynamically switches its regulatory program between the chilling and recovery phases. During chilling stress, it accumulates in the nucleus and activates chilling-related genes to enhance chilling tolerance. During recovery, it directly activates the nitrogen transporter gene OsNRT2.4 while repressing OsTCP19, thereby enhancing nitrogen use efficiency and promoting tiller regeneration.
"To evaluate the breeding potential of this molecular module, we established a novel phenotyping system for chilling resilience to test the breeding potential of CHPOjap, which is of critical importance for agricultural applications," Prof. CHONG said.
Following chilling stress, plants were allowed to recover under different nitrogen conditions before being transplanted to the field for yield evaluation. Under all nitrogen treatments, CHPOjap-overexpressing plants consistently produced higher grain yield per plant and exhibited greater nitrogen use efficiency than wild-type plants, while chpo mutants showed the opposite phenotype.
The findings demonstrated the robust breeding potential of CHPOjap as a molecular module for molecular-design breeding aimed at improving yield and nitrogen use efficiency under post-chilling conditions.
The study uncovers the molecular mechanism that coordinates chilling resilience with nitrogen use efficiency. It also provides a genetic explanation for the long-standing agricultural practice of applying nitrogen fertilizer to promote tiller regrowth after chilling stress. In addition, it offers a molecular module and breeding strategy for developing climate-resilient rice varieties with stable yield and efficient nitrogen utilization.
Journal
Nature
Article Title
CHPO coordinates chilling recovery and nitrogen use in rice
Article Publication Date
17-Jun-2026
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