Systems and methods for extracting rare earth elements with engineered microorganisms

Modified bacteria for use in bioleaching rare earth elements (REEs) from a composition comprising the REEs, the modified bacteria comprising at least one engineered genetic change that is correlated with improved bioleaching of the REEs, relative to REE bioleaching by unmodified bacteria of the same species as the modified bacteria, and wherein the at least one genetic change comprises a change that results in decreased expression, or increased expression, of at least one gene, and wherein the at least one gene optionally encodes a protein that participates phosphate-specific transport system signaling, or encodes a protein that participates in pyrroloquinoline quinone (PQQ) synthesis.