Methanogenic archaeal communities in rice roots grown in flooded soil pots: Estimation by PCR-DGGE and sequence analyses

Methanogenic archaeal communities in rice roots (endorhizosphere and rhizoplane) were studied based on the analysis of the polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) patterns of 16S rDNA and sequence analysis of DNA extracts from nodal roots of rice plants grown in flooded soil pots. DGGE patterns of the methanogenic archaeal communities were similar among the root samples, irrespective of the growth stage and emergence node, which indicated that specific methanogenic archaeal members inhabited rice roots constantly. As the DGGE bands from the methanogenic archaeal members were detected in young nodal roots soon after emergence at the early stage of rice growth, the presence of anoxic sites in young roots was estimated. Root age also affected the methanogenic archaeal communities in rice roots based on the changes in the DGGE patterns among nodal roots at the early stage of rice growth. All the sequenced clones belonged to Methanomicrobiales and Rice cluster I that had been assumed to be one of the uncultured methanogenic archaeal members.