Molecular Soil Biology 2026, Vol.17, No.1, 12-25 http://bioscipublisher.com/index.php/msb 13 International Rice Research Institute commonly uses a reference line of about 15 cm below the field surface and monitors water level changes by inserting perforated tubes. Many field studies have summarized data from 1990 to 2024, and the general results are relatively consistent: compared with continuous flooding, AWD can significantly reduce methane emissions and also lower the combined warming potential of CH4 andN2O (Jiang et al., 2022). However, the situation is not entirely uniform; in some areas, N2O emissions may increase, and the effect is also influenced by many factors, such as soil dryness, the frequency of wetting and drying, local precipitation and temperature, soil organic carbon, pH, and nitrogen application levels. Precisely because of this, when discussing irrigation methods now, the focus has gradually shifted from "whether to dry" to more detailed questions, such as to what water level to dry, at which growth stage to do it, and how to coordinate with nutrient management. In many past studies on greenhouse gas emissions from paddy fields, attention was often focused solely on the changes in the abundance of a certain type of functional microorganism, using it to explain the gas flux. However, in a system like soil where multiple processes occur simultaneously, this perspective is actually a bit simplistic: whether different groups change together and what resources or electron flows they might be linked through are also worthy of attention. Thus, the method of co-occurrence networks has gradually been introduced. Researchers first used high-throughput sequencing data to attempt to reconstruct the association relationships between different groups or genes, and then used indicators such as node degree, clustering coefficient, and modularity to describe the network structure. However, the amplification data itself has a relative abundance limitation, which can easily lead to false correlations. Therefore, some more robust inference methods have been developed later, such as SparCC for compositional data and SPIEC-EASI based on conditional independence relationships. With this network framework, people can not only see the influence of environmental selection but also discuss potential interactions and the position of key groups in the functional process, making paddy field methane research no longer rely solely on scattered indicators but closer to an understanding of the overall structure. 2 Theoretical Foundation and Research Hypotheses 2.1 Microbiological mechanism of methane generation and oxidation in paddy soil The amount of methane emitted from paddy fields is not determined by a single process. It can be roughly regarded as the cumulative result of "generation, oxidation and transport". The lower layer of the soil is anaerobic, where methanogenic archaea produce methane; but in the surface layer or near the rice roots, there is oxygen, and some methane will be consumed by methane-oxidizing bacteria. When these processes occur simultaneously, the remaining methane will enter the atmosphere through the rice ventilation structure, bubbling or diffusion (Nazaries et al., 2017). The stratified structure formed after flooding - the surface layer prefers oxygen, the lower part prefers anaerobic conditions, and the rhizosphere micro-region - precisely allows these processes to occur simultaneously at different locations. In research, some molecular markers are commonly used to track related microorganisms. For example, the mcrA gene encodes the alpha subunit of methanocoumarin reductase and is a key enzyme in the final step of methane production, and is usually regarded as a functional marker for methanogenic archaea; while pmoA is often used to describe the phylogeny and potential functions of aerobic methane-oxidizing bacteria. Some studies have proposed that the abundance of mcrA and pmoA, as well as their ratio, often provide clues for determining the source and sink relationship of soil methane (Tveit et al., 2019). However, it should be noted that simply looking at the gene quantity cannot directly indicate the flux size; it is necessary to combine environmental conditions and actual processes for understanding. 2.2 Mechanism of soil redox environment regulation by irrigation modes Many discussions will mention that when the irrigation method changes, the methane process also changes. The key lies in the fact that the soil's redox state is re-adjusted. During continuous flooding, the soil's Eh often remains at a relatively low level, and there are fewer available electron acceptors. As a result, the anaerobic processes such as fermentation, nutrient synthesis, and methane production tend to be more dominant (Conrad et al., 2020). However, if alternate wetting and drying irrigation is adopted, the situation is quite different: after the field surface
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