Fungus and bacterium, which could grow under acidic conditions, were isolated, and their characteristics of growth and neutralization of acids were studied. They could grow in acidic media (pH 4.0) containing several kinds of acids at the same rate in the medium of pH 7.2 and neutralize acids. For bioremediation of pollutants in soil, we proposed a self-immobilization method of microorganisms forming aggregates in a shallow layer of soil. These isolated strains, which showed weak aggregation and were different in size, were successfully co-immobilized with Bacillus subtilis secreting viscous polymer in a shallow layer of model soil packed in a column and could neutralize acidic solutions flowing through packed soil.