Mining rare earth elements with ammonium sulfate as a leaching agent provokes a significant perturbation in soil...

The mining of rare earth elements (REEs), which are critical for modern technologies, frequently leads to severe soil degradation, particularly through ammonium sulfate-based in-situ leaching. This study provided a comprehensive metagenomic assessment of how REEs mining reshapes soil ecosystems. We analyzed paired samples from a mined site and an adjacent unmined control in a typical ion-adsorption REEs deposit region in China. Mining activity was associated with profound alterations in soil geochemical profiles. While soil pH decreased from 4.72 to 4.42, total carbon (TC) declined by over two-thirds (from 1.05 to 0.31 g kg^-1), and total nitrogen (TN) exhibited a significant 22% increase (from 215.60 to 263.26 mg kg^-1). Regarding REEs, mining caused an approximately 53% reduction in their total content (from 475.83 to 218.82 mg kg^-1) and a restructured composition (cerium from 28% to 75%, lanthanum from 23% to 5.4%, and neodymium from 18% to 4.8%). Metagenomic analysis revealed that microbial diversity was significantly lower in the post-mining area compared to the unmined control. Bacterial communities shifted from a balanced composition to an oligotroph-dominated state, with p_Acidobacteriota increasing to 41% and the copiotrophic p_Actinomycetota declining from 23% to 10%. Fungal communities transitioned from a p_Basidiomycota-rich (31%) symbiotic state to an p_Ascomycota-dominated (77%), saprotrophic condition. Mantel tests and path analysis identified the mining-induced deterioration of soil physicochemical and nutrient properties (especially pH, TC, and Mg) as a key factor associated with microbial restructuring, rather than REEs depletion itself. Functionally, Kyoto Encyclopedia of Genes and Genomes annotation revealed a widespread suppression of metabolic pathways critical for ecosystem functioning, including C fixation, N metabolism, energy production, and environmental adaptation. The identification of key microbial taxa (e.g., declining p_Actinomycetota and p_Chloroflexota) as biomarkers for soil health, and their strong linkage to decreased C and N cycling functions, offers potential genomic targets for monitoring and guiding the recovery of soil ecosystem services in post-mining landscapes.