Ion adsorption-type heavy rare earths found in southern China are important ore resources, whose yttrium(Y)-group rare-earth elements account for 90% of the total mass of rare earths known on the planet. At present, ammonia-nitrogen wastewater from extraction of rare earths pose threats to the environment. A bacterial strain (Bacillus sp. ZD 1) isolated from the “Foot Cave” mining area was used for adsorption of Y³⁺. Its adsorption capacity reached 428 μmol/g when the initial concentration of Y³⁺ was 1.13 mM. Moreover, 50 mg of Bacillus sp. ZD 1 (converted to dry mass) could completely adsorb Y³⁺ in the mother solution of mixed rare earths from the rare-earth mining area. Ammonia nitrogen in the remaining solution after adsorption was removed through denitrification using a fungus named Galactomyces sp. ZD 27. The final concentration of ammonia nitrogen in wastewater was lower than Indirect Emission Standard of Pollutants for Rare-earth Industry (GB 26451-2011). Furthermore, the resulting fungal cells of Galactomyces sp. ZD 27 could be used to produce single cell proteins, whose content accounted for 70.75% of the dry mass of cells. This study offers a new idea for integrated environmentally-friendly extraction and ecological restoration of the mining area in southern China.

To address yttrium (Y) contamination from ion adsorption mining, this study developed a combined microbial phytoremediation strategy for dual objectives: ensuring crop safety in Lactuca sativa and enhancing Y recovery by Solanum nigrum. Two specific microbial consortia were constructed from rare earth tailings isolates: inoculant I (bacterial: Enterobacter sp., Serratia sp., Bacillus sp.) applied to L. sativa, and inoculant II (fungal: Penicillium sp., Aspergillus sp., Talaromyces sp.) applied to S. nigrum. Inoculant I increased L. sativa biomass by 26% while reducing Y content in roots and rhizosphere soil solution by 47% and 56%, respectively, potentially through down-regulation of amino acid metabolites. Inoculant II increased Y content in the S. nigrum rhizosphere soil solution by 89%, linked to up-regulation of organic acids and coumarin derivatives. Both consortia reduced plant stress markers and enhanced soil enzyme activities. These findings demonstrate that specialized microbial consortia can differentially regulate Y behavior in the rhizosphere—immobilizing it in a crop for food safety, while enhancing its bioavailability for a hyperaccumulator—offering a targeted strategy for managing rare earth element-contaminated agricultural soils.