###### Abstract  
Rice paddies are dynamic areas for microbe-mediated nitrogen cycling and this could be driven by the long-term alteration of paddy soil edaptic factors. The objective of this study is to evaluate the lasting impact of long-term compost fertilization on the soil chemical properties of paddy fields, determining the size of the microbial guilds involved in nitrification and denitrification. Soil sampling was done on paddy fields without fertilizer, with NPR + compost, and with compost application, and the soil chemical properties of the fields were determined from 2018 to 2021. The abundance of genes related to nitrogen cycling was measured using quantitative PCR (qPCR). Annual analyses showed that the studied soils have attained stable, baseline chemical properties with significantly increased phosphorus (P20S), potassium (K), SOM, and total nitrogen (TN) due to decades of fertilization with NPK + compost and compost. Consequently, the genes related to bacterial amoA, nosZI, and nosZII were significantly increased in Com- and NPKCom-amended soils compared to the NF paddy field. The mirK gene abundance was unaffected after long-term amendment with compost. A positive correlation was found between the archaeal amoA gene abundance and DOC, while SOM and TN were consistently positively correlated with the abundances of bacterial amoA, nosZI, and nosZII genes, in addition to interactions with potassium and DOC. Principal component analysis (PCA) indicated soil variabilities across treatments, where the unfertilized paddy field contained lower SOM and nutrient contents with a characteristic mirK gene abundance. Similar variabilities in terms of the SOM, TN, K, nosZI, and nosZII gene abundances were observed in the Com and NPKCom paddy fields. Long-term amendment with NPK + compost and compost created soil paddy fields with stable soil chemical properties with higher SOM and nutrient contents, which established higher abundances of genes associated with denitrification and nitrification that were observed during the fallow period. long-term compost fertilization; nitrogen cycle; nitrification; denitrification; gene abundance; soil chemical properties +
Footnote †: journal: Applied  
are connected to the changes and disturbances in these processes due to inappropriate use and the imbalance of diverse nitrogen compounds, leading to negative consequences. To prevent further environmental issues and to improve the conditions of our agroecosystems, obtaining detailed information about the interactions of nitrogen cycling-related microorganisms with soils and the different disturbances requires understanding and investigation [2]. Nitrogen immobilization into crops is the main goal of fertilizer application; however, nitrogen fertilization has become a potent source for nitrogen transformation processes in soil, particularly nitrification and denitrification [3]. Long-term fertilization and the selection of fertilizer sources are important to maximize nutrient efficiency [4]. To predict soil productivity and understand critical processes and linkages in soil, predicting long-term changes in the microbial composition and structure over extended periods is critical [5]. For instance, the ammonia-oxidizing clades at the genus level responded differently to long-term inorganic nitrogen amendment in paddy fields [6]. Long-term nitrogen application also led to taxon-specific responses in the different microbial guilds associated with nitrogen cycling microbial communities [2]. The 16S rRNA is the most-commonly utilized microbial indicator to research structure, composition, and diversity. However, difficulty in the detection of less abundant and less dominant microbial groups performing common functions can occur using 16S rRNA gene-based probes. An alternative technique is to use functional gene markers that provide greater resolution below the species level.