Molecular Soil Biology 2026, Vol.17, No.1, 12-25 http://bioscipublisher.com/index.php/msb 12 Research Insight Open Access Effects of Irrigation Patterns on Soil Microbial Network Structure and Methanogenic Pathways in Subtropical Paddy Fields Zhongxian Li, Ruchun Chen, Haiying Huang Hier Rice Research Center, Hainan Institute of Tropical Agricultural Resources, Sanya, 572025, Hainan, China Corresponding email: haiying.huang@hitar.org Molecular Soil Biology, 2026, Vol.17, No.1 doi: 10.5376/msb.2026.17.0002 Received: 25 Dec., 2025 Accepted: 30 Jan., 2026 Published: 11 Feb., 2026 Copyright © 2026 Li et al., This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Li Z.X., Chen R.C., and Huang H.Y., 2026, Effects of irrigation patterns on soil microbial network structure and methanogenic pathways in subtropical paddy fields, Molecular Soil Biology, 17(1): 12-25 (doi: 10.5376/msb.2026.17.0001) Abstract Paddy fields in subtropical regions are constantly submerged in water, which can easily lead to a strong reducing environment, making methane-producing bacteria active and increasing methane emissions. However, in the context of increasingly scarce water resources and the continuous emphasis on the "dual carbon" goals, people have begun to pay more attention to alternate wetting and drying (AWD) irrigation, which is believed to save water and potentially reduce emissions. However, the situation is not that simple: some studies combining field experiments, meta-analyses, and multi-omics results have found that the microbial community, key functional genes, and network structure all change under different irrigation patterns. Generally speaking, compared with continuous flooding, AWD can significantly reduce methane emissions and lower the overall warming potential, but sometimes N₂O emissions increase, and the effect is also influenced by factors such as temperature, precipitation, soil organic carbon, and pH. In field practice, the often-mentioned "safe AWD", such as refilling water when the water level drops to about -15 cm, can generally ensure yield while saving water and reducing methane emissions. From a microbial perspective, the periodic changes in water can alter soil Eh and substrate supply, causing the methane-producing related groups and their connections to readjust. These changes often correspond to the variations in gas fluxes and also provide some references for paddy field water management. Keywords Alternate wetting and drying (AWD); Subtropical paddy fields; Microbial co-occurrence network; mcrA/pmoA; Methane production pathway 1 Introduction Rice paddies can actually be regarded as a kind of long-term managed wetland. Once watered, the oxygen in the soil is quickly consumed, and the environment gradually becomes anoxic. Various anaerobic decomposition processes become active, and methane becomes one of the important end products. However, the internal environment of the rice paddy is not entirely uniform. Early microbiological studies have found that flooded rice paddies are more like systems divided into several small "compartments": the surface layer often has a little oxygen, the lower layer is mostly anaerobic, and the rhizosphere and rhizoplane of rice form special micro-zones. Oxygen, nitrate, and methane often show obvious micro-scale gradients in these places. Because of this, methane production and methane oxidation often coexist and are significantly influenced by environmental conditions (Kögel-Knabner et al., 2021). From this perspective, rice paddies are not only like a continuously operating biogeochemical reaction field but are also often used to observe the relationship between microbial community structure and ecological function. For subtropical rice-growing areas, the climate is hot and humid, the multiple cropping index is high, and organic matter input and farming activities are relatively frequent. Therefore, methane emissions from rice paddies are not only related to climate change but also to regional ecological security and the transformation of agriculture towards a green approach (Li et al., 2022). Rice production has always been inseparable from irrigation. The traditional approach is continuous flooding (CF), which indeed helps suppress weeds and ensure stable yields, but the cost is also obvious: it consumes a large amount of water and the long-term waterlogging makes the soil more oxygen-deficient, increasing the risk of methane emissions (Zhang et al., 2019). In recent years, under the dual pressure of water resource constraints and emission reduction requirements, alternate wetting and drying (AWD) irrigation has gradually been promoted. Simply put, it involves allowing the field to periodically dry to a certain water level before re-flooding. The
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