Community structure of eukaryotes in rice roots estimated by PCR-DGGE pattern and sequence analyses

Abstract

The community structure of eukaryotes and representative members in rice roots (endorhizosphere and rhizoplane) was estimated based on the analysis of polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) patterns of 18S rDNA, followed by sequence analysis of characteristic DGGE bands. Rice plants were grown in flooded soil pots, and rice roots were separately collected according to the nodal position of their emergence three times during rice cultivation. The number of DGGE bands in the first / oldest nodal roots which had emerged during the upland nursery stage was remarkably higher than that of the bands in the other nodal roots which emerged after transplanting. Statistical analysis enabled to separate the first nodal roots from the other nodal roots, and thereafter all the other nodal roots which emerged on July 2 and 21 from those which emerged on Sept. 12. The closest relatives corresponding to the DGGE bands that characterized the first nodal roots were Mastigomycotina, Mastigophorea, Chlorophycota, and Ciliophora, while those corresponding to the bands that characterized the other nodal roots which emerged on July 2 and July 21 were Oomycetes (Mastigomycotina) and Mastigophorea. In contrast, all the closest relatives corresponding to the bands that characterized the roots which emerged on Sept. 12 were fungi (Ascomycotina and Mastigomycotaina). Polymyxa graminis (Myxomycota) was detected in all the nodal roots which emerged on July 2 but only in the first nodal roots which emerged on July 21. P. graminis did not appear to colonize rice roots under flooded conditions.