Extraction of rare earths from ion-adsorption type rare earth ore by indigenous microbial community

• Indigenous microbial communities cultured in nutrient broth (NB) medium exhibited high diversity and secreted organic acids (citric, malic, gluconic, itaconic) that enhance rare earth leaching from ion-adsorption type ores. • Stirred bioleaching achieved leaching rates of 92.49% for La, 92.42% for Ce, and 94.39% for Y under optimized conditions (70vol% inoculum, 5.0 mL·g−1 liquid–solid ratio, 60 min), with leaching efficiency fitting a Poly5 polynomial function (R² > 0.99). • Column bioleaching at 1 kg scale achieved a rare earth leaching rate of 98.88% after 117 hours, driven by a self-propelled low-pH environment. • XRD and SEM analyses revealed mineralogical changes post-bioleaching, including increased wave intensity of quartz, kaolinite, orthoclase, and muscovite, and decreased zeolite, indicating dissolution of fine clay particles and providing insights into the bioleaching mechanism.