Ion-adsorption rare earth element (REE) deposits are the main reservoirs of REEs worldwide, and are widely exploited in South China. Microbial diversity is essential for maintaining the performance and function of mining ecosystems. Investigating the ecological patterns underlying the REE mine microbiome is essential to understand ecosystem responses to environmental changes and to improve the bioremediation of mining areas. We applied 16S rRNA and ITS gene sequence analyses to investigate the composition characteristics of prokaryotic (bacteria, archaea) and fungal communities in a river impacted by REE acid mine drainage (REE-AMD). The river formed a unique micro-ecosystem, including the main prokaryotic taxa of Proteobacteria, Acidobacteria, Crenarchaeota, and Euryarchaeota, as well as the main fungal taxa of Ascomycota, Basidiomycota, and Chytridiomycota. Analysis of microbial diversity showed that, unlike prokaryotic communities that responded drastically to pollution disturbances, fungal communities were less affected by REE-AMD, but fluctuated significantly in different seasons. Ecological network analysis revealed that fungal communities have lower connectivity and centrality, and higher modularity than prokaryotic networks, indicating that fungal communities have more stable network structures. The introduction of REE-AMD mainly reduced the complexity of the community network and the number of keystone species, while the proportion of negative prokaryotic–fungal associations in the network increased. Ecological process analysis revealed that, compared to the importance of environmental selection for prokaryotes, stochastic processes might have contributed primarily to fungal communities in REE mining areas. These findings confirm that the different assembly mechanisms of prokaryotic and fungal communities are key to the differences in their responses to environmental perturbations. The findings also provide the first insights into microbiota assembly patterns in REE-AMD and important ecological knowledge for the formation and development of microbial communities in REE mining areas.

离子吸附型稀土元素（REE）矿床是世界范围内稀土元素的主要储层，在华南地区得到广泛开发。微生物多样性对于维持采矿生态系统的性能和功能至关重要。研究 REE 矿山微生物组的生态模式对于了解生态系统对环境变化的响应和改善矿区的生物修复至关重要。我们应用 16S rRNA 和 ITS 基因序列分析来研究受 REE 酸性矿山排水 (REE-AMD) 影响的河流中原核生物（细菌、古生菌）和真菌群落的组成特征。河流形成了独特的微生态系统，包括变形菌门、酸杆菌门、Crenarchaeota和Euryarchaeota的主要原核生物分类群，以及子囊菌门、担子菌门和壶菌门的主要真菌类群. 微生物多样性分析表明，与对污染干扰反应剧烈的原核生物群落不同，真菌群落受 REE-AMD 的影响较小，但在不同季节波动显着。生态网络分析表明，真菌群落比原核生物网络具有较低的连通性和中心性，模块化程度较高，表明真菌群落具有更稳定的网络结构。REE-AMD的引入主要降低了群落网络的复杂性和关键物种的数量，而网络中负原核-真菌关联的比例增加。生态过程分析表明，与环境选择对原核生物的重要性相比，随机过程可能主要促成了 REE 矿区的真菌群落。这些发现证实，原核和真菌群落的不同组装机制是它们对环境扰动反应差异的关键。这些发现还提供了对 REE-AMD 中微生物群组装模式的初步见解，以及对 REE 矿区微生物群落形成和发展的重要生态知识。