Cyanobacterial inoculation modifies the rhizosphere microbiome of rice planted to a tropical alluvial soil

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 and 45 DAT. The concentrations of total PLFAs ranged from 33.3 to 103.5 nmol g−1 on 15 DAT, which declined on 45 DAT in the rhizosphere (33.8 nmol g−1) compared to the bulk soil (193 nmol g−1) with cyanobacterial inoculation. On 45 DAT, PLFAs comprised 30-40% polyunsaturated fatty acids, followed by straight chain fatty acids (20-29%) and monounsaturated fatty acids (7-18%). Cyanobacterial inoculation led to decreased presence of Gram-positive bacteria, Gram-negative bacteria, anaerobe and actinobacteria with 1.1-1.5 folds decrease on 45 DAT. This was also evident from the principal component analysis of PLFA based community profiles. These observations clearly demonstrated that cyanobacteria characteristically affected the microbial communities of soils under both unsterilized and sterilized conditions, and influenced plant growth positively.