Abstract
In this study, bacterial communities in a lab-scale substrate treatment system and wastewater treatment plant were investigated. Used methods were polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and sequencing of DNA gene fragments from DGGE gels. In PCR-DGGE, used primer regions were two, the V1-V3 region and the V3-V5 region. For these sequencing results, the ratios of bacterial detection by PCR-DGGE were compared with the expected value of bacterial detection in the Ribosomal Database Project II (RDP II). In these results, it was considered that there are relation between the expected value of bacterial detection in RDP II and the ratio of bacterial detection by PCR-DGGE and sequencing in this research region. When the expected value in RDP II in the V1-V3 region was lower than 104, the ratio of bacterial detection by PCR-DGGE was lower than 0.07. When the expected value was greater than 104, the ratio of bacterial detection by DGGE ranged from 0 to 0.14. The expected value in RDP II in the V3-V5 was over 0.5 × 104,, the ratio of bacterial detection by PCR-DGGE was expected to rise. As same way, when it was lower than 0.5 × 104, it was lower than 0.05. It was considered that to check the expected value of bacterial detection in RDP II was useful to preliminary examination before PCR-DGGE analysis. In the region which sequencing or molecular cloning was difficult, these researches were helpful in metagenomic studies.
