Community structure of microeukaryotes in a rice rhizosphere revealed by DNA-based PCR-DGGE

Abstract

Rice roots provide a specific habitat for microorganisms in the rhizosphere of a submerged field through supply of oxygen and organic matter. Many studies have focused on the microbial community in the rice rhizosphere, but less is still known about the microeukaryotic community structure of rice rhizosphere. This study explored the microeukaryotic community structure of a rice rhizosphere through denaturing gradient gel electrophoresis (DGGE) targeting 18S rRNA gene. The rice roots and the rhizosphere soil samples, which were collected from a field under rice-wheat rotation system, were separately analyzed. To characterize the rice rhizosphere-specific community, the bulk soil of rice field and the wheat rhizosphere samples were also examined. DGGE fingerprints showed that the microeukaryotic community of rice roots were distinct from the community of the bulk soil and showed a temporal shift with the growth stage. The rhizosphere soil community was distinct from the root and bulk soil communities, but this could be explained by that the root and bulk soil communities were shared in the rhizosphere. The rice rhizosphere community was also distinct from those in the wheat rhizosphere. Microeukaryotes that characterized the rice rhizosphere (roots and the rhizosphere soil) community could be affiliated to Polymyxa, flagellates, and oomycetes, which suggested that microeukaryotes with various ecological roles, e.g., parasites, bacterial grazers, and decomposers, inhabit the rice rhizosphere. The results showed that the rice root and its growth stages are key factors shaping the microeukaryotic community structure in the rhizosphere.