Characterization of depth-related microbial community structure in lake sediment by denaturing gradient gel electrophoresis of amplified 16S rDNA and reversely transcribed 16S rRNA fragments

Abstract

Vertical changes of bacterial community structure in a mesophilic lake sediment were investigated by denaturing gradient gel electrophoresis (DGGE) of amplified 16S rDNA and reversely transcribed 16S rRNA fragments. Comparison of community structure analyses based on 16S rDNA and rRNA revealed that the diversity indices from the 16S rDNA-based DGGE profiles were greater than those from the 16S rRNA-based DGGE profiles. In addition, the diversity indices based on 16S rDNA did not change drastically throughout the layers, but the diversity indices based on 16S rRNA decreased with sediment depth. This result indicates that the diversity of active bacteria decreases and inactive bacteria accumulate in association with sedimentation. Dendrograms deduced from DGGE profiles of either 16S rDNA or rRNA were different, and the rRNA-based dendrogram showed a significant difference between the upper layers (0–2, 2–5, and 5–8 cm) and lower layers (8–11, 11–14, 14–17, and 17–20 cm). The sequences of 13 DGGE bands were determined. Phylogenetic analysis of these rDNA fragments revealed that the most conspicuous band in both rDNA- and rRNA-based DGGE was closely related to the genus Nitrospira (95% sequence similarity), and the relative signal intensity was strong especially in the deep layers. Membrane hybridization with a probe targeting the genus Nitrospira also supported the observation that 16S rRNAs derived from Nitrospira-like microorganisms were abundant in this sediment (8.6–16.8% of bacterial 16S rRNA) and that the relative abundance increased with depth. Overall, our results demonstrated that parallel characterization of community structure based on both 16S rDNA and rRNA is important for assessing whole microbial populations and active microbial populations in sediments.