Molecular analyses reveal stability of bacterial communities in bulk soil of a Japanese paddy field: Estimation by denaturing gradient gel electrophoresis of 16S rRNA genes amplified from DNA accompanied with RNA
KIKUCHI, Hiroyasu | Watanabe, Takeshi | JIA, Zhongjun | Kimura, Makoto | ASAKAWA, Susumu
Dominant bacterial communities in the bulk soil of the plow layer in a Japanese paddy field were investigated over 1 year using denaturing gradient gel electrophoresis (DGGE) of 16S rRNA genes, and the succession and phylogenetic composition of the bacterial communities were estimated. "Existing" bacterial communities in the plow layer soil estimated from DNA were stable over 1 year irrespective of the soil conditions, although multivariate analysis of the DGGE patterns showed a difference in the communities between flooded and drained/upland conditions. Metabolically "active" bacterial communities based on the RNA analysis were also stable and all the bands detected in the DNA analysis existed, indicating that most of the bacterial members in the "existing" communities could be metabolically "active" in the plow layer soil. The DGGE bands that were commonly present and characteristic of certain periods were closely related to Chloroflexi, Actionobacteria, Alphaproteobacteria, Verrucomicrobia, Acidobacteria, Nitrospira, Chlorobi, Cyanobacteria and candidate division OP10, and most of their closest relatives were uncultured bacteria. Comparisons of these bacterial members in the bulk soil with those in other habitats in the plow layer showed that the bacterial members in the bulk soil comprised more diverse phylogenetic groups at phylum or class levels than those in other habitats. Heterogeneous and oligotrophic features of the soil may have enabled diverse and versatile bacterial members to grow and survive in the bulk soil.
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