Ecological Imprint of Rare Earth Mining on Microbial Communities and Water Quality Across Depth and Distance Gradients in Ganzhou, China

Rare earth element (REE) mining exerts profound impacts on aquatic ecosystems, yet the microbial community responses and water quality under such stress remain underexplored. In this study, the surface (0.2 m) and subsurface (1.0 m) water along a spatial transect from proximal to distal points was investigated in a REE-mining area of Ganzhou, China. Physicochemical analyses revealed pronounced gradients of nitrogen (e.g., NH₄⁺-N, NO₃^--N), heavy metals (e.g., Mn, Zn, Pb), and REEs (e.g., La, Nd, Ce), with higher accumulation near mining sources and partial attenuation downstream. Dissolved oxygen and redox potential indicated mildly reducing conditions at contaminated points, potentially promoting denitrification and altering nitrogen cycling. Metagenomic sequencing showed significant shifts in microbial community composition, with enrichment of metal- and nitrogen-tolerant taxa, and key denitrifiers (e.g., <i>Acidovorax</i>, <i>Bradyrhizobium</i>, <i>Rhodanobacter</i>), particularly at upstream polluted points. KEGG-based gene annotation highlighted dynamic nitrogen transformations mediated by multiple pathways, including nitrification, denitrification, dissimilatory nitrate reduction to ammonium, and nitrogen fixation. Notably, genes associated with nitrite and nitrate reduction (e.g., <i>nir</i>, <i>nar</i>, <i>nrf</i>) were enriched near mining sources, indicating enhanced nitrogen conversion potential, while downstream activation of nitrogen-fixing genes suggested partial ecosystem recovery. Meanwhile, some microbial such as <i>Variovorax</i> carried metal tolerant genes (e.g., <i>ars</i>, <i>chr</i>, <i>cnr</i>). These findings demonstrate that REE and heavy metal contamination restructure microbial networks, modulate nitrogen cycling, and create localized ecological stress gradients. This study provides a comprehensive assessment of mining-related water pollution, microbial responses, and ecological risks, offering valuable insights for monitoring, restoration, and sustainable management of REE-impacted aquatic environments.