Community structure of the microbiota in the floodwater of a Japanese paddy field estimated by restriction fragment length polymorphism and denaturing gradient gel electrophoresis pattern analyses

The polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and PCR-denaturing gradient gel electrophoresis (DGGE) patterns of 16S rDNA were studied to elucidate the effects of the type of fertilization and the growth stage of rice plants on the community structure of the microbiota in the floodwater of a Japanese paddy field under a long-term fertilizer trial. From the mid tillering stage, a higher pH and temperature were observed in the plot without fertilization (NoF plot) than in the plots supplied with chemical fertilizers (CF plot) and with compost (CM plot). DNA fragments specific to the respective plots and common to every plot were detected after the digestion of PCR products by restriction enzymes. Cluster analysis separated the RFLP and DGGE patterns of the microbiota in the floodwater into four clusters; the microbiota in (1) the NoF plot, (2) the CF plot, (3) the CM plot, and (4) the CF and CM plots in the early growing stage. The effect of fertilizer application on the community structure was more conspicuous than that of seasonal variation.