Soil microbial community changed due to the application of a biological fertilizer EM-$Bokashi^{TM}$ and microwave radiation. Root colonization of sugar beet by Pseudomonas fluorescens DR54 was enhanced in sterilized soil but not in soils amended with EM-Bokashi. Therefore, EM-Bokashi can be a potential means to alter soil microbial diversity and soil sterilization can be a practical means to enhance plant root colonization by microbial inoculants under controlled conditions such as nursery and greenhouse crops.