Study on rhizosphere bacterial community in lowland rice grown with organic fertilizers by using PCR-denaturing gradient gel electrophoresis

Abstract

For the promotion of environment-friendly agriculture, use of organic fertilizers and green materials is increasingly attempted in rice farming. Although effects of organic fertilizers on soil bacteria in the rhizosphere can differ from those in non-rhizosphere soil, microbiological studies that specifically address the rice rhizosphere still limited. This study was undertaken to investigate the impact of organic fertilizers on soil bacteria communities through comparison of rhizosphere soils and bulk soils. Effects of soil types and seasonal change were also analyzed. Rice plants (Oryza sativa L. cv. Nipponbare) were cultivated in a lowland paddy field of Andosol soil. Applications of compost and rice bran in combination with chemical fertilizer were compared with control soil (chemical fertilizer only). Soil 16S rDNA extracted from rhizosphere soil collected using ultrasonic treatment of rice roots and from bulk soils were analyzed using PCR-denaturing gradient gel electrophoresis (DGGE). Principal component analysis based on PCR-DGGE profiles revealed clear differences in the community structures of soil bacteria between rhizosphere and bulk soils. Furthermore, rhizosphere bacterial community structures of compost and rice bran treatments were plainly different from that of control, and changed with the seasons. The organic fertilizers showed pronounced effects on bacterial communities until mid-summer, but small effects in autumn. Results of this study suggest that the rhizosphere microorganisms in paddy fields can be modified through organic fertilizer management. Moreover, effects of organic fertilizer application, soil type, and phenology on soil bacteria appear depending on interaction with the rice rhizosphere effects in paddy fields.