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Cyanobacteria are novel means of influencing rice plant growth and development. Therefore, the objective was to investigate the effect of Calothrix elenkinii inoculation on rice growth and microbiome using unsterilized and sterilized soils. The microbial community profiles generated by denaturing gradient gel electrophoresis (DGGE) and phospholipid fatty acids (PLFA) analyses, and the relationships between the rice plant growth and soil functioning were examined on 15 and 45 days after transplanting (DAT). Cyanobacterial inoculation brought about growth stage dependent increases in plant biomass (up to 70%) and nitrogenase activity (about 48%). Although the PCR-DGGE bacterial community profiles showed the effect of cyanobacterial inoculation on the soil microbiome, the PLFA based community profiles showed distinct spatial and temporal changes, both in the bulk and rhizosphere soils sampled on 15 …