Microbial diversity in lake sediments detected by PCR-DGGE |
| |
Authors: | Xinqing Zhao Liuyan Yang Can Chen Lin Xiao Lijuan Jiang Zhe Ma Haowei Zhu Zhenyang Yu and Daqiang Yin |
| |
Institution: | (1) State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210093, China |
| |
Abstract: | In this study, PCR-denaturing gradient gel electrophoresis (DGGE) was applied to analyze the microbial communities in lake
sediments from Lake Xuanwu, Lake Mochou in Nanjing and Lake Taihu in Wuxi. Sediment samples from seven locations in three
lakes were collected and their genomic DNAs were extracted. The DNA yields of the sediments of Lake Xuanwu and Lake Mochou
were high (10 μg/g), while that of sediments in Lake Taihu was relatively low. After DNA purification, the 16S rDNA genes
(V3 to V5 region) were amplified and the amplified DNA fragments were separated by parallel DGGE. The DGGE profiles showed
that there were five common bands in all the lake sediment samples indicating that there were similarities among the populations
of microorganisms in all the lake sediments. The DGGE profiles of Lake Xuanwu and Lake Mochou were similar and about 20 types
of microorganisms were identified in the sediment samples of both lakes. These results suggest that the sediment samples of
these two city lakes (Xuanwu, Mochou) have similar microbial communities. However, the DGGE profiles of sediment samples in
Lake Taihu were significantly different from these two lakes. Furthermore, the DGGE profiles of sediment samples in different
locations in Lake Taihu were also different, suggesting that the microbial communities in Lake Taihu are more diversified
than those in Lake Xuanwu and Lake Mochou. The differences in microbial diversity may be caused by the different environmental
conditions, such as redox potential, pH, and the concentrations of organic matters. Seven major bands of 16S rDNA genes fragments
from the DGGE profiles of sediment samples were further re-amplified and sequenced. The results of sequencing analysis indicate
that five sequences shared 99%–100% homology with known sequences (Bacillus and Brevibacillus, uncultured bacteria), while the other two sequences shared 93%–96% homology with known sequences (Acinetobacter, and Bacillus). The study shows that the PCR-DGGE technique combined with sequence analysis is a feasible and efficient method for the
determination of microbial communities in sediment samples.
__________
Translated from Acta Ecologica Sinica, 2006, 26(11): 3610–3616 译自: 生态学报] |
| |
Keywords: | Sediment microbial diversity denaturing gradient gel electrophoresis (DGGE) 16S ribosome DNA (16S rDNA) sequence |
本文献已被 SpringerLink 等数据库收录! |
|