An integrated rice–fish farming system is an efficient technique used to maintain water quality and rice/fish productivity. In addition to fish and rice plants that have mutually beneficial ecological roles, bacteria play important roles in maintaining water quality and soil fertility. Therefore, this study investigated the diversity and dynamic change in the bacterial community composition of water and sediment in an integrated rice–fish farming system using a high-throughput sequencing approach. The 16S rRNA gene of bacteria was amplified, and the IonS5™XL sequencing platform was used to identify bacterial community during the cultivation period. The results demonstrated that fishpond, rice field and trench sediment samples were dominated by the phyla Proteobacteria (60.9%–64.4%), Acidobacteria (8.7%) and Chloroflexi (6.3%), whereas water samples were dominated by the phyla Proteobacteria (65.7%), Bacteroidetes (17.1%) and Actinobacteria (8.5%). The dynamics of the bacterial community composition of the water and sediment samples were clearly observed at phylum and genus levels respectively. Water temperature (34.67°C) and ammonia-nitrogen content (0.38 mg L⁻¹) at the early stage of cultivation correlated with the abundances of Actinobacteia and Cyanobacteria at the phylum level and Acinetobacter at the genus level. Furthermore, several bacterial genera could potentially contribute to the biogeochemical cycle. In particular, Sorangium was involved in organic matter degradation, Methylophilus was implicated in nitrification, Novosphingobium and Methylotenera were essential for denitrification, and Desulfobacca was important for sulfate reduction. This study improved our understanding of the bacterial community in the integrated rice–fish farming system and provided data for further development.

中文翻译：

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印度尼西亚日惹 Sleman 稻鱼综合养殖系统中细菌群落的动态变化

综合稻田养鱼系统是一种用于保持水质和稻田/鱼类生产力的有效技术。除了具有互利生态作用的鱼类和水稻外，细菌在维持水质和土壤肥力方面也发挥着重要作用。因此，本研究使用高通量测序方法研究了稻-鱼综合养殖系统中水和沉积物细菌群落组成的多样性和动态变化。扩增细菌16S rRNA基因，利用IonS5™XL测序平台对培养期间细菌群落进行鉴定。结果表明，鱼塘、稻田和沟渠沉积物样品以变形菌门（60.9%~64.4%）、酸菌门（8.7%）和绿屈菌门（6.3%）为主，而水样以变形菌门（65.7%）、拟杆菌门（17.1%）和放线菌门（8.5%）为主。分别在门和属水平上清楚地观察到水和沉积物样品的细菌群落组成的动态。水温 (34.67°C) 和氨氮含量 (0.38 mg L^-1 ) 在培养的早期阶段与门水平的放线菌和蓝细菌的丰度和属水平的不动杆菌的丰度相关。此外，几种细菌属可能有助于生物地球化学循环。特别是，纤维堆囊参与有机物降解，食甲基硝化被牵连，Novosphingobium和Methylotenera分别进行反硝化至关重要，Desulfobacca是为硫酸盐还原重要。这项研究提高了我们对稻-鱼综合养殖系统中细菌群落的了解，并为进一步发展提供了数据。