Rice Genomics and Genetics 2025, Vol.16, No.3, 116-131 http://cropscipublisher.com/index.php/rgg 122 nutrient release, it may also accelerate the loss of certain nutrients, such as ammonia volatilization and runoff loss. Therefore, it needs to be regulated through field management. For example, the depth of the water layer and the exchange rate of water flow should be reasonably controlled to both utilize animal disturbance to release nutrients and prevent nutrients from being lost with the water flow. Experiments have shown that in the rice-shrimp co-cultivation system, ditching shrimp in the water layer of rice fields can help reduce the ammonia volatilization flux of rice fields, and even under higher nitrogen application conditions, ammonia losses have not increased. This may be because the ditch area absorbs some ammonia, and the activity of shrimp makes the nitrogen cycle in the water body more complicated, thereby reducing the peak ammonia loss. Other studies have shown that rice-fish co-cultivation can reduce the accumulation of nitrate nitrogen in field surface water and reduce the risk of leaching to groundwater through the ecological effects of water bodies (Lan et al., 2021). The disturbance mechanism of animals on water and soil makes rice field integrated farming a dynamically stirred nutrient reactor: on the one hand, it accelerates the flow of nutrients between soil and plants, and on the other hand, it also requires us to manage carefully to prevent excessive nutrient loss. 4.3 Changes in microbial communities and enzymatic activities The regulation of soil nutrient cycling by rice field integrated farming is largely achieved by affecting soil microbial communities and their functions. Soil microorganisms are the drivers of nutrient decomposition and transformation, and their community structure and activity determine key processes such as the decomposition rate of organic matter, nitrogen mineralization, and phosphorus dissociation. Under integrated farming conditions, the soil microbial environment undergoes many changes, thereby regulating nutrient cycling. First, the number and biomass of microorganisms have increased significantly. As mentioned above, the rice-fish-rice-duck system has observed an increase in soil microbial biomass carbon and nitrogen (SMBC/SMBN), and an increase in the total phosphatidic acid (PLFA) content of the microbial community. Li et al. (2025) conducted a long-term experiment in two places and found that after 30 years of rice-fish farming, the total amount of soil microorganisms was about 1.5 times that of the single-crop control, and the number of various microorganisms such as fungi, bacteria, and actinomycetes increased across the board. The increase in the number of microorganisms means that more "workers" are involved in the degradation of organic matter and nutrient transformation, making the soil nutrient supply more active and stable. Second, the structure of the microbial community has been adjusted. Integrated farming often promotes the improvement of bacterial diversity and changes the relative abundance of dominant groups. For example, Liao et al. (2019) found that the Shannon diversity index of soil bacteria and fungal communities under rice-duck farming conditions was higher than that of conventional rice fields. At the same time, rice-fish farming is conducive to a moderate increase in the fungus/bacteria ratio. The increase in the proportion of fungi in long-term farming soils is conducive to the formation of more stable humus (fungi have a strong ability to decompose lignin, which is conducive to the decomposition of difficult-to-degrade organic matter). In the bacterial community, some functional bacteria related to nitrogen cycle are significantly enriched. For example, Liu et al. (2024) reported that rice-fish farming promoted the reproduction of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in the soil, thereby improving the effectiveness of soil nitrogen supply. AOA and AOB are key bacterial groups in the nitrification process. Their increase means that ammonium nitrogen is converted into nitrate nitrogen more quickly, and the efficiency of plant absorption or further conversion is improved. This is one of the microscopic mechanisms for the accelerated nitrogen conversion in integrated farming. Third, soil enzyme activity is significantly enhanced. Soil enzymes are products and mediators of microbial metabolism and are directly involved in the decomposition of organic nutrients. In the integrated farming system, due to the rich matrix and active microorganisms, the activity of various nutrient conversion enzymes is generally improved. Yan et al. (2023) observed that the activities of urease, sucrase, phosphatase and other enzymes in the rice-duck-shrimp farming soil were more than 20% higher than those in
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