Multi-omics insights into rare earth element recovery by microalgae under salinity gradients

Conventional rare earth element (REE) extraction methods are resource-intensive and generate secondary pollutants, whereas biomining using microorganisms such as microalgae offers a more sustainable alternative. Microalgal growth and metal recovery are strongly influenced by environmental factors, especially salinity; however, the molecular mechanisms driving REE recovery in microalgae exposed to saline conditions remain largely unexplored. The overarching aim of this study is to elucidate the effects of salinity on REE recovery by microalgae using a multi-omics framework. Specifically, nine microalgal strains were screened across salinities of 0-5 %, followed by integrated metabolomic, transcriptomic, and proteomic characterization of Limnospira maxima under control, REE-only, 3.5 % salinity, and combined REE-salinity conditions. Among the tested species, L. maxima exhibited the highest REE recovery efficiency, outperforming other microalgae by a factor of 2-10. In L. maxima, heavy REE (Sc, Y, Tb, and Dy) were recovered 10-15 % more efficiently than light REE (La, Pr, Nd), particularly under salinities between 0.5 % and 5 %. The selective recovery of REE by L. maxima was most pronounced at elevated salinities. Global metabolomic profiles of the combined treatment were primarily associated with salinity, suggesting that salinity establishes the dominant physiological state within which REE-associated responses occur. Multi-omics analysis showed distinct responses to REE and salinity stress, including changes in carbon fixation, photosynthesis, and amino acid and lipid metabolism, with both transcript-protein convergence and pathway-level discordance indicating complex cross-layer regulation. Overall, the results identify L. maxima as a promising candidate for REE recovery under saline conditions while defining molecular responses and knowledge gaps relevant to future development of microalgae-based REE separation.