Succession and Phylogenetic Profile of Eubacterial Communities in Rice Straw Incorporated into a Rice Field: Estimation by PCR-DGGE Analysis

Abstract

PCR-DGGE analysis followed by sequencing was conducted to estimate the succession and the phylogenetic profile of the eubacterial communities responsible for the decomposition of rice straw (RS) that was incorporated into a rice field. Leaf sheath and leaf blade parts were separately put in nylon mesh bags, and were placed in the rice field soil under drained conditions during the off-cropping season and under flooded conditions after transplantation of rice. In addition, RS samples that had been placed under drained conditions in the off-cropping season were placed again in flooded rice field soil after transplantation of rice. DGGE patterns of the bacterial communities in the RS samples were classified into two groups, namely leaf sheaths and leaf blades. Principal component analysis of the DGGE patterns revealed the succession along with the duration of placement. These results indicated that the RS part (sheath or blade) mainly determined the structure of the bacterial communities responsible for the RS decomposition, followed by the duration of placement. Sequence analysis of the characteristic DGGE bands indicated that most of the closest relatives associated with the bands belonged to α-, β-, γ-, and δ-Proteobacteria, CFB group, and Spirochaetes. Some bands were closely related to Acidobacteria and Verrucomicrobia. CFB members and α-Proteobacteria predominated commonly in both RS parts, while γ- and δ-Proteobacteria, and Spirochaetes and β-Proteobacteria specifically colonized sheath and blade parts, respectively. In addition, Proteobacteria and CFB members characterized the differences in the bacterial communities under flooded or drained conditions. These results suggest that Proteobacteria, CFB group, and Spirochaetes were responsible for RS decomposition in rice field soil under both flooded and drained conditions.